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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
<a href="Bio.expressions.blast-module.html">Package blast</a> ::
Module ncbiblast
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ncbiblast</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html">source code</a></span></p>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="Number"></a><span class="summary-sig-name">Number</span>(<span class="summary-sig-arg">name</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">attrs</span>=<span class="summary-sig-default"><code class="variable-group">{</code><code class="variable-group">}</code></span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#Number">source code</a></span>
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<td><span class="summary-sig"><a name="_nv"></a><span class="summary-sig-name">_nv</span>(<span class="summary-sig-arg">s</span>,
<span class="summary-sig-arg">expr</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#_nv">source code</a></span>
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<td><span class="summary-sig"><a name="float_stat"></a><span class="summary-sig-name">float_stat</span>(<span class="summary-sig-arg">name</span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#float_stat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_num_stat"></a><span class="summary-sig-name">_num_stat</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">signed</span>,
<span class="summary-sig-arg">comma</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#_num_stat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="int_stat"></a><span class="summary-sig-name">int_stat</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">signed</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">comma</span>=<span class="summary-sig-default">0</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#int_stat">source code</a></span>
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<td><span class="summary-sig"><a name="int_param"></a><span class="summary-sig-name">int_param</span>(<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">signed</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">comma</span>=<span class="summary-sig-default">0</span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#int_param">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="float_param"></a><span class="summary-sig-name">float_param</span>(<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#float_param">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a name="_bit_info"></a><span class="summary-sig-name">_bit_info</span>(<span class="summary-sig-arg">s</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.blast.ncbiblast-pysrc.html#_bit_info">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
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<td align="left"><span class="table-header">Variables</span></td>
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<a name="spaces_line"></a><span class="summary-name">spaces_line</span> = <code title="Opt(Spaces())+ AnyEol()">Opt(Spaces())+ AnyEol()</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blast_filter" class="summary-name">blast_filter</a> = <code title="Str("BLASTN", "BLASTP", "BLASTX", "TBLASTX", "TBLASTN")">Str("BLASTN", "BLASTP", "BLASTX", "TBLASTX", "T<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#ncbi_version" class="summary-name">ncbi_version</a> = <code title="Std.application_version(Group("appversion", Re(r"2.\d+\.\d+")))">Std.application_version(Group("appversion", Re(<code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastn_appheader" class="summary-name">blastn_appheader</a> = <code title="Std.application_name(Str("BLASTN"), {"app": "blastn"})+ Str(" ")+ ncbi\
_version+ Str(" ")+ ToEol()">Std.application_name(Str("BLASTN"), {"app":<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastp_appheader" class="summary-name">blastp_appheader</a> = <code title="Std.application_name(Str("BLASTP"), {"app": "blastp"})+ Str(" ")+ ncbi\
_version+ Str(" ")+ ToEol()">Std.application_name(Str("BLASTP"), {"app":<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastx_appheader" class="summary-name">blastx_appheader</a> = <code title="Std.application_name(Str("BLASTX"), {"app": "blastx"})+ Str(" ")+ ncbi\
_version+ Str(" ")+ ToEol()">Std.application_name(Str("BLASTX"), {"app":<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastn_appheader" class="summary-name">tblastn_appheader</a> = <code title="Std.application_name(Str("TBLASTN"), {"app": "tblastn"})+ Str(" ")+ nc\
bi_version+ Str(" ")+ ToEol()">Std.application_name(Str("TBLASTN"), {"app<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastx_appheader" class="summary-name">tblastx_appheader</a> = <code title="Std.application_name(Str("TBLASTX"), {"app": "tblastx"})+ Str(" ")+ nc\
bi_version+ Str(" ")+ ToEol()">Std.application_name(Str("TBLASTX"), {"app<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#query_letters" class="summary-name">query_letters</a> = <code title="Spaces()+ Str("(")+ Std.query_size(Digits())+ Str(" letters)")+ AnyEol\
()+ Assert(AnyEol())">Spaces()+ Str("(")+ Std.query_size(Digits())+ <code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="query_descr"></a><span class="summary-name">query_descr</span> = <code title="Std.query_description_block(query_descr)">Std.query_description_block(query_descr)</code>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="_comma_digits"></a><span class="summary-name">_comma_digits</span> = <code title="Re(r"\d(\d\d?)?(,\d\d\d)+")">Re(r"\d(\d\d?)?(,\d\d\d)+")</code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#query_database" class="summary-name">query_database</a> = <code title="Str("Database:")+ Opt(Spaces())+ Std.database_name(UntilEol())+ AnyEol\
()+ Spaces()+ Std.database_num_sequences(Number(), {"bioformat:decode"\
: "int.comma"})+ Str(" sequences;")+ Spaces()+ Std.database_num_letter\
s(Number(), {"bioformat:decode": "int.comma"})+ Spaces()+ Str("total l\
etters")+ ToEol()">Str("Database:")+ Opt(Spaces())+ Std.database<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#to_table" class="summary-name">to_table</a> = <code title="Group("to_table", (SkipLinesUntil(Str("Sequences producing significant\
"))+ ToEol()+ AnyEol()))">Group("to_table", (SkipLinesUntil(Str("Sequences pr<code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#table_entry" class="summary-name">table_entry</a> = <code title="Std.search_table_entry(Group("table_entry", (AssertNot(AnyEol())+ Std.\
search_table_description(Re(r".{66}"))+ Spaces()+ Std.search_table_val\
ue(Float(), {"name": "score", "bioformat:decode": "float"})+ Spaces()+\
Std.search_table_value(Float(), {"name": "evalue", "bioformat:decode"\
: "float"})+ AnyEol())))">Std.search_table_entry(Group("table_entry", (Ass<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="table"></a><span class="summary-name">table</span> = <code title="Std.search_table(Rep(table_entry))">Std.search_table(Rep(table_entry))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#header" class="summary-name">header</a> = <code title="Std.search_header(SkipLinesUntil(Str("Query="))+ query_descr+ query_le\
tters+ AnyEol()+ Group("to_database", NullOp())+ query_database+ Opt(t\
o_table+ table)+ SkipLinesUntil(Str(">")))">Std.search_header(SkipLinesUntil(Str("Query="))+ quer<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#hit_length" class="summary-name">hit_length</a> = <code title="Spaces()+ Str("Length = ")+ Std.hit_length(Digits())+ AnyEol()+ Opt(Sp\
aces())+ AnyEol()">Spaces()+ Str("Length = ")+ Std.hit_length(Digits<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#hit_descr" class="summary-name">hit_descr</a> = <code title="Str(">")+ Std.hit_description(UntilEol())+ AnyEol()+ Rep(AssertNot(hit\
_length)+ Std.hit_description(UntilEol())+ AnyEol())">Str(">")+ Std.hit_description(UntilEol())+ AnyEol(<code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#num_bits" class="summary-name">num_bits</a> = <code title="Std.hsp_value(Float(), {"name": "bits", "bioformat:decode": "float",})">Std.hsp_value(Float(), {"name": "bits", "bioformat:<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#expect" class="summary-name">expect</a> = <code title="Std.hsp_value(Float(), {"name": "expect", "bioformat:decode": "float"}\
)">Std.hsp_value(Float(), {"name": "expect", "bioformat:<code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#num_identical" class="summary-name">num_identical</a> = <code title="Std.hsp_value(Digits(), {"name": "identical", "bioformat:decode": "int\
"})">Std.hsp_value(Digits(), {"name": "identical", <code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#hsp_length" class="summary-name">hsp_length</a> = <code title="Std.hsp_value(Digits(), {"name": "length", "bioformat:decode": "int"})">Std.hsp_value(Digits(), {"name": "length", "biofo<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#num_positives" class="summary-name">num_positives</a> = <code title="Std.hsp_value(Digits(), {"name": "positives", "bioformat:decode": "int\
"})">Std.hsp_value(Digits(), {"name": "positives", <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#score" class="summary-name">score</a> = <code title="Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d+)\), Expect = *\
")+ expect+ AnyEol()">Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastn_score" class="summary-name">tblastn_score</a> = <code title="Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d+)\), " r"Expect\
(\((?P<expect_num>\d+)\))? = *")+ expect+ AnyEol()">Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastn_identical" class="summary-name">blastn_identical</a> = <code title="Re(r" *Identities = *")+ num_identical+ Str("/")+ hsp_length+ ToEol()">Re(r" *Identities = *")+ num_identical+ Str<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastp_identical" class="summary-name">blastp_identical</a> = <code title="Re(r" *Identities = *")+ num_identical+ Str("/")+ hsp_length+ ToSep(se\
p= ",")+ Re(" Positives = *")+ num_positives+ ToEol()">Re(r" *Identities = *")+ num_identical+ Str<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#frame" class="summary-name">frame</a> = <code title="Str(" Frame = ")+ Std.hsp_frame(UntilEol(), {"which": "query"})+ AnyEo\
l()">Str(" Frame = ")+ Std.hsp_frame(UntilEol(), {"which": <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastx_frame" class="summary-name">tblastx_frame</a> = <code title="Str(" Frame = ")+ Std.hsp_frame(UntilSep(sep= " "), {"which": "query"}\
)+ Str(" / ")+ Std.hsp_frame(UntilEol(), {"which": "subject"})+ AnyEol\
()">Str(" Frame = ")+ Std.hsp_frame(UntilSep(sep= <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#strand" class="summary-name">strand</a> = <code title="Re(r" *Strand = ")+(Std.hsp_strand(Str("Plus"), {"strand": "+1", "whic\
h": "query"}) | Std.hsp_strand(Str("Minus"), {"strand": "-1", "which":\
"query"}))+ Str(" / ")+(Std.hsp_strand(Str("Plus"), {"strand": "+1", \
"which": "subject"}) | Std.hsp_strand(Str("Minus"), {"strand": "-1", "\
which": "subject"}))+ AnyEol()">Re(r" *Strand = ")+(Std.hsp_strand(Str("Plus"), {"str<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#query_line" class="summary-name">query_line</a> = <code title="Std.hsp_seqalign_query_leader(Std.hsp_seqalign_query_name(Str("Query")\
)+ Re(": *")+ Std.hsp_seqalign_query_start(Digits())+ Re(" *"))+ Std.h\
sp_seqalign_query_seq(UntilSep(sep= " "))+ Re(" *")+ Std.hsp_seqalign_\
query_end(Digits())+ AnyEol()">Std.hsp_seqalign_query_leader(Std.hsp_seqalign_qu<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#homology_line" class="summary-name">homology_line</a> = <code title="Std.hsp_seqalign_homology_seq(Str(" ")+ UntilEol())+ AnyEol()">Std.hsp_seqalign_homology_seq(Str(" ")+ Un<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#subject_line" class="summary-name">subject_line</a> = <code title="Std.hsp_seqalign_subject_name(Str("Sbjct"))+ Re(": *")+ Std.hsp_seqali\
gn_subject_start(Digits())+ Re(" *")+ Std.hsp_seqalign_subject_seq(Unt\
ilSep(sep= " "))+ Re(" *")+ Std.hsp_seqalign_subject_end(Digits())+ An\
yEol()">Std.hsp_seqalign_subject_name(Str("Sbjct"))+ Re<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastn_hsp_header" class="summary-name">blastn_hsp_header</a> = <code title="score+ blastn_identical+ strand+ spaces_line+ spaces_line">score+ blastn_identical+ strand+ spaces_li<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastp_hsp_header"></a><span class="summary-name">blastp_hsp_header</span> = <code title="score+ blastp_identical+ spaces_line">score+ blastp_identical+ spaces_line</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastx_hsp_header"></a><span class="summary-name">blastx_hsp_header</span> = <code title="score+ blastp_identical+ frame+ spaces_line">score+ blastp_identical+ frame+ spaces_line</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastn_hsp_header" class="summary-name">tblastn_hsp_header</a> = <code title="tblastn_score+ blastp_identical+ frame+ spaces_line">tblastn_score+ blastp_identical+ frame+ s<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastx_hsp_header" class="summary-name">tblastx_hsp_header</a> = <code title="tblastn_score+ blastp_identical+ tblastx_frame+ spaces_line+ spaces_li\
ne">tblastn_score+ blastp_identical+ tblastx_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#alignment" class="summary-name">alignment</a> = <code title="Std.hsp_seqalign(query_line+ homology_line+ subject_line+ Rep1(spaces_\
line))">Std.hsp_seqalign(query_line+ homology_line+ subjec<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="hsp"></a><span class="summary-name">hsp</span> = <code title="Std.hsp(Group("hsp_header", NullOp())+ Rep(alignment))">Std.hsp(Group("hsp_header", NullOp())+ Rep(alignment))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="hit"></a><span class="summary-name">hit</span> = <code title="Std.hit(hit_descr+ hit_length+ Rep(Group("hsp", hsp)))">Std.hit(hit_descr+ hit_length+ Rep(Group("hsp", hsp)))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#db_stats" class="summary-name">db_stats</a> = <code title="Str(" Database:")+ ToEol()+ Str(" Posted date:")+ ToEol()+ Str(" \
Number of letters")+ ToEol()+ Str(" Number of sequences")+ ToEol()+ s\
paces_line">Str(" Database:")+ ToEol()+ Str(" Posted date:"<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#ungapped_lambda_stats" class="summary-name">ungapped_lambda_stats</a> = <code title="Str("Lambda K H")+ AnyEol()+(Spaces()+ float_stat("lambda")+ \
Spaces()+ float_stat("k")+ Spaces()+ float_stat("h")+ ToEol())">Str("Lambda K H")+ AnyEol()+(<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#gapped_lambda_stats" class="summary-name">gapped_lambda_stats</a> = <code title="Opt(Str("Gapped")+ AnyEol())+ Str("Lambda K H")+ AnyEol()+(Sp\
aces()+ float_stat("gapped_lambda")+ Spaces()+ float_stat("gapped_k")+\
Spaces()+ float_stat("gapped_h")+ ToEol())">Opt(Str("Gapped")+ AnyEol())+ Str("Lambd<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#lambda_stats" class="summary-name">lambda_stats</a> = <code title="ungapped_lambda_stats+ AnyEol()+ gapped_lambda_stats">ungapped_lambda_stats+ AnyEol()+ gapped_lambda_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#matrix_stats" class="summary-name">matrix_stats</a> = <code title="SkipLinesUntil(Str("Matrix:"))+ _nv("Matrix: ", Std.search_statistic(U\
ntilEol(), {"name": "matrix"}))">SkipLinesUntil(Str("Matrix:"))+ _nv("Matrix: ",<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#gap_penalties_stats" class="summary-name">gap_penalties_stats</a> = <code title="_nv("Gap Penalties: Existence: ", int_param("existence_gap_penalty")+ \
Str(", Extension: ")+ int_param("extension_gap_penalty"))">_nv("Gap Penalties: Existence: ", int_pa<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#generic_info1" class="summary-name">generic_info1</a> = <code title="_nv("Number of Hits to DB: ", int_stat("num_hits_to_db", signed= 1))+ \
_nv("Number of Sequences: ", int_stat("num_sequences"))+ _nv("Number o\
f extensions: ", int_stat("num_extensions"))+ _nv("Number of successfu\
l extensions: ", int_stat("num_successful_extensions"))+ _nv("Number o\
f sequences better than 10.0: ", int_stat("num_sequences_better_than_1\
0"))">_nv("Number of Hits to DB: ", int_stat("num_hi<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#generic_info2" class="summary-name">generic_info2</a> = <code title="_nv("length of query: ", int_stat("query_length"))+ _nv("length of dat\
abase: ", int_stat("database_length", comma= 1))+ _nv("effective HSP l\
ength: ", int_stat("effective_hsp_length"))+ _nv("effective length of \
query: ", int_stat("effective_query_length"))+ _nv("effective length o\
f database: ", int_stat("effective_database_length", comma= 1))+ _nv("\
effective search space: ", int_stat("effective_search_space"))+ _nv("e\
ffective search space used: ", int_stat("effective_search_space_used")\
)">_nv("length of query: ", int_stat("query_lengt<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#hsp_info" class="summary-name">hsp_info</a> = <code title="_nv("Number of HSP's better than 10.0 without gapping: ", int_stat("nu\
m_hsps_better_than_10_without_gapping"))+ _nv("Number of HSP's success\
fully gapped in prelim test: ", int_stat("num_hsps_successfully_gapped\
_in_prelim_test"))+ _nv("Number of HSP's that attempted gapping in pre\
lim test: ", int_stat("num_hsps_attempted_gapping_in_prelim_test"))+ _\
nv("Number of HSP's gapped (non-prelim): ", int_stat("num_hsps_gapped"\
))">_nv("Number of HSP's better than 10.0 without gappi<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#frameshift_info" class="summary-name">frameshift_info</a> = <code title="_nv("frameshift window, decay const: ", int_stat("frameshift_window")+\
Re(r", *")+ float_stat("frameshift_decat_const"))">_nv("frameshift window, decay const: ", int_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="t_info"></a><span class="summary-name">t_info</span> = <code title="_nv("T: ", int_stat("t"))">_nv("T: ", int_stat("t"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="a_info"></a><span class="summary-name">a_info</span> = <code title="_nv("A: ", int_stat("1"))">_nv("A: ", int_stat("1"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="x1_info"></a><span class="summary-name">x1_info</span> = <code title="_bit_info("X1: ", "x1")">_bit_info("X1: ", "x1")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="x2_info"></a><span class="summary-name">x2_info</span> = <code title="_bit_info("X2: ", "x2")">_bit_info("X2: ", "x2")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="x3_info"></a><span class="summary-name">x3_info</span> = <code title="_bit_info("X3: ", "x3")">_bit_info("X3: ", "x3")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="s1_info"></a><span class="summary-name">s1_info</span> = <code title="_bit_info("S1: ", "s1")">_bit_info("S1: ", "s1")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="s2_info"></a><span class="summary-name">s2_info</span> = <code title="_bit_info("S2: ", "s2")">_bit_info("S2: ", "s2")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastn_ending" class="summary-name">blastn_ending</a> = <code title="db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf\
o1+ Opt(hsp_info)+ generic_info2+ t_info+ a_info+ x1_info+ x2_info+ s1\
_info+ s2_info">db_stats+ lambda_stats+ matrix_stats+ gap_pena<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastp_ending" class="summary-name">blastp_ending</a> = <code title="db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf\
o1+ hsp_info+ generic_info2+ t_info+ a_info+ x1_info+ x2_info+ x3_info\
+ s1_info+ s2_info">db_stats+ lambda_stats+ matrix_stats+ gap_pena<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastx_ending" class="summary-name">blastx_ending</a> = <code title="db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf\
o1+ hsp_info+ generic_info2+ frameshift_info+ t_info+ a_info+ x1_info+\
x2_info+ x3_info+ s1_info+ s2_info">db_stats+ lambda_stats+ matrix_stats+ gap_pena<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastn_ending" class="summary-name">tblastn_ending</a> = <code title="db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf\
o1+ hsp_info+ generic_info2+ frameshift_info+ t_info+ a_info+ x1_info+\
x2_info+ x3_info+ s1_info+ s2_info">db_stats+ lambda_stats+ matrix_stats+ gap_pen<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastx_ending" class="summary-name">tblastx_ending</a> = <code title="db_stats+ ungapped_lambda_stats+ matrix_stats+ generic_info1+ generic_\
info2+ frameshift_info+ t_info+ a_info+ x1_info+ x2_info+ s1_info+ s2_\
info">db_stats+ ungapped_lambda_stats+ matrix_stats<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#format" class="summary-name">format</a> = <code title="Std.record(Group("appheader", NullOp())+ header+ Rep(hit)+ Group("endi\
ng", NullOp()))">Std.record(Group("appheader", NullOp())+ header+ Rep(<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastn" class="summary-name">blastn</a> = <code title="replace_groups(format, (("appheader", blastn_appheader), ("hsp_header"\
, blastn_hsp_header), ("ending", blastn_ending)))">replace_groups(format, (("appheader", blastn_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastp" class="summary-name">blastp</a> = <code title="replace_groups(format, (("appheader", blastp_appheader), ("hsp_header"\
, blastp_hsp_header), ("ending", blastp_ending)))">replace_groups(format, (("appheader", blastp_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#blastx" class="summary-name">blastx</a> = <code title="replace_groups(format, (("appheader", blastx_appheader), ("hsp_header"\
, blastx_hsp_header), ("ending", blastx_ending)))">replace_groups(format, (("appheader", blastx_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastn" class="summary-name">tblastn</a> = <code title="replace_groups(format, (("appheader", tblastn_appheader), ("hsp_header\
", tblastn_hsp_header), ("ending", tblastn_ending)))">replace_groups(format, (("appheader", tblastn_apphea<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#tblastx" class="summary-name">tblastx</a> = <code title="replace_groups(format, (("appheader", tblastx_appheader), ("hsp_header\
", tblastx_hsp_header), ("ending", tblastx_ending)))">replace_groups(format, (("appheader", tblastx_apphea<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.ncbiblast-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
<type 'exceptions.DeprecationWarning'>,
2): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="blast_filter"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blast_filter</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("BLASTN", "BLASTP", "BLASTX", "TBLASTX", "TBLASTN")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="ncbi_version"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ncbi_version</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_version(Group("appversion", Re(r"2.\d+\.\d+")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("BLASTN"), {"app": "blastn"})+ Str(" ")+ ncbi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_version+ Str(" ")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("BLASTP"), {"app": "blastp"})+ Str(" ")+ ncbi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_version+ Str(" ")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("BLASTX"), {"app": "blastx"})+ Str(" ")+ ncbi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_version+ Str(" ")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("TBLASTN"), {"app": "tblastn"})+ Str(" ")+ nc<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
bi_version+ Str(" ")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("TBLASTX"), {"app": "tblastx"})+ Str(" ")+ nc<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
bi_version+ Str(" ")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query_letters"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query_letters</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("(")+ Std.query_size(Digits())+ Str(" letters)")+ AnyEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()+ Assert(AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query_database"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query_database</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Database:")+ Opt(Spaces())+ Std.database_name(UntilEol())+ AnyEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()+ Spaces()+ Std.database_num_sequences(Number(), {"bioformat:decode"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
: "int.comma"})+ Str(" sequences;")+ Spaces()+ Std.database_num_letter<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s(Number(), {"bioformat:decode": "int.comma"})+ Spaces()+ Str("total l<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
etters")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="to_table"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">to_table</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("to_table", (SkipLinesUntil(Str("Sequences producing significant<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"))+ ToEol()+ AnyEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="table_entry"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">table_entry</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.search_table_entry(Group("table_entry", (AssertNot(AnyEol())+ Std.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
search_table_description(Re(r".{66}"))+ Spaces()+ Std.search_table_val<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ue(Float(), {"name": "score", "bioformat:decode": "float"})+ Spaces()+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Std.search_table_value(Float(), {"name": "evalue", "bioformat:decode"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
: "float"})+ AnyEol())))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.search_header(SkipLinesUntil(Str("Query="))+ query_descr+ query_le<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tters+ AnyEol()+ Group("to_database", NullOp())+ query_database+ Opt(t<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
o_table+ table)+ SkipLinesUntil(Str(">")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hit_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hit_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("Length = ")+ Std.hit_length(Digits())+ AnyEol()+ Opt(Sp<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
aces())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hit_descr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hit_descr</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(">")+ Std.hit_description(UntilEol())+ AnyEol()+ Rep(AssertNot(hit<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_length)+ Std.hit_description(UntilEol())+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="num_bits"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">num_bits</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_value(Float(), {"name": "bits", "bioformat:decode": "float",})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="expect"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">expect</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_value(Float(), {"name": "expect", "bioformat:decode": "float"}<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="num_identical"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">num_identical</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_value(Digits(), {"name": "identical", "bioformat:decode": "int<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hsp_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hsp_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_value(Digits(), {"name": "length", "bioformat:decode": "int"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="num_positives"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">num_positives</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_value(Digits(), {"name": "positives", "bioformat:decode": "int<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d+)\), Expect = *<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ expect+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ num_bits+ Re(r" bits \((?P<XXX1>\d+)\), " r"Expect<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(\((?P<expect_num>\d+)\))? = *")+ expect+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_identical"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_identical</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = *")+ num_identical+ Str("/")+ hsp_length+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp_identical"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp_identical</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = *")+ num_identical+ Str("/")+ hsp_length+ ToSep(se<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
p= ",")+ Re(" Positives = *")+ num_positives+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="frame"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">frame</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(" Frame = ")+ Std.hsp_frame(UntilEol(), {"which": "query"})+ AnyEo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx_frame"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx_frame</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(" Frame = ")+ Std.hsp_frame(UntilSep(sep= " "), {"which": "query"}<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Str(" / ")+ Std.hsp_frame(UntilEol(), {"which": "subject"})+ AnyEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="strand"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">strand</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Strand = ")+(Std.hsp_strand(Str("Plus"), {"strand": "+1", "whic<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
h": "query"}) | Std.hsp_strand(Str("Minus"), {"strand": "-1", "which":<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"query"}))+ Str(" / ")+(Std.hsp_strand(Str("Plus"), {"strand": "+1", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"which": "subject"}) | Std.hsp_strand(Str("Minus"), {"strand": "-1", "<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
which": "subject"}))+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_seqalign_query_leader(Std.hsp_seqalign_query_name(Str("Query")<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Re(": *")+ Std.hsp_seqalign_query_start(Digits())+ Re(" *"))+ Std.h<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sp_seqalign_query_seq(UntilSep(sep= " "))+ Re(" *")+ Std.hsp_seqalign_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
query_end(Digits())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="homology_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">homology_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_seqalign_homology_seq(Str(" ")+ UntilEol())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="subject_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">subject_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_seqalign_subject_name(Str("Sbjct"))+ Re(": *")+ Std.hsp_seqali<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
gn_subject_start(Digits())+ Re(" *")+ Std.hsp_seqalign_subject_seq(Unt<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ilSep(sep= " "))+ Re(" *")+ Std.hsp_seqalign_subject_end(Digits())+ An<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
yEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
score+ blastn_identical+ strand+ spaces_line+ spaces_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
tblastn_score+ blastp_identical+ frame+ spaces_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
tblastn_score+ blastp_identical+ tblastx_frame+ spaces_line+ spaces_li<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ne
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="alignment"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">alignment</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.hsp_seqalign(query_line+ homology_line+ subject_line+ Rep1(spaces_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="db_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">db_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(" Database:")+ ToEol()+ Str(" Posted date:")+ ToEol()+ Str(" <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Number of letters")+ ToEol()+ Str(" Number of sequences")+ ToEol()+ s<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
paces_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="ungapped_lambda_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ungapped_lambda_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Lambda K H")+ AnyEol()+(Spaces()+ float_stat("lambda")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Spaces()+ float_stat("k")+ Spaces()+ float_stat("h")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="gapped_lambda_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">gapped_lambda_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Opt(Str("Gapped")+ AnyEol())+ Str("Lambda K H")+ AnyEol()+(Sp<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
aces()+ float_stat("gapped_lambda")+ Spaces()+ float_stat("gapped_k")+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Spaces()+ float_stat("gapped_h")+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="lambda_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">lambda_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ungapped_lambda_stats+ AnyEol()+ gapped_lambda_stats
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="matrix_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">matrix_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
SkipLinesUntil(Str("Matrix:"))+ _nv("Matrix: ", Std.search_statistic(U<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ntilEol(), {"name": "matrix"}))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="gap_penalties_stats"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">gap_penalties_stats</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
_nv("Gap Penalties: Existence: ", int_param("existence_gap_penalty")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Str(", Extension: ")+ int_param("extension_gap_penalty"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="generic_info1"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">generic_info1</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
_nv("Number of Hits to DB: ", int_stat("num_hits_to_db", signed= 1))+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_nv("Number of Sequences: ", int_stat("num_sequences"))+ _nv("Number o<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
f extensions: ", int_stat("num_extensions"))+ _nv("Number of successfu<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l extensions: ", int_stat("num_successful_extensions"))+ _nv("Number o<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
f sequences better than 10.0: ", int_stat("num_sequences_better_than_1<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
0"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="generic_info2"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">generic_info2</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
_nv("length of query: ", int_stat("query_length"))+ _nv("length of dat<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
abase: ", int_stat("database_length", comma= 1))+ _nv("effective HSP l<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ength: ", int_stat("effective_hsp_length"))+ _nv("effective length of <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
query: ", int_stat("effective_query_length"))+ _nv("effective length o<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
f database: ", int_stat("effective_database_length", comma= 1))+ _nv("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
effective search space: ", int_stat("effective_search_space"))+ _nv("e<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ffective search space used: ", int_stat("effective_search_space_used")<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hsp_info"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hsp_info</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
_nv("Number of HSP's better than 10.0 without gapping: ", int_stat("nu<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
m_hsps_better_than_10_without_gapping"))+ _nv("Number of HSP's success<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
fully gapped in prelim test: ", int_stat("num_hsps_successfully_gapped<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_in_prelim_test"))+ _nv("Number of HSP's that attempted gapping in pre<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
lim test: ", int_stat("num_hsps_attempted_gapping_in_prelim_test"))+ _<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nv("Number of HSP's gapped (non-prelim): ", int_stat("num_hsps_gapped"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="frameshift_info"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">frameshift_info</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
_nv("frameshift window, decay const: ", int_stat("frameshift_window")+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Re(r", *")+ float_stat("frameshift_decat_const"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_ending"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_ending</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
o1+ Opt(hsp_info)+ generic_info2+ t_info+ a_info+ x1_info+ x2_info+ s1<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_info+ s2_info
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp_ending"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp_ending</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
o1+ hsp_info+ generic_info2+ t_info+ a_info+ x1_info+ x2_info+ x3_info<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ s1_info+ s2_info
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_ending"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_ending</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
o1+ hsp_info+ generic_info2+ frameshift_info+ t_info+ a_info+ x1_info+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
x2_info+ x3_info+ s1_info+ s2_info
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_ending"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_ending</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
db_stats+ lambda_stats+ matrix_stats+ gap_penalties_stats+ generic_inf<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
o1+ hsp_info+ generic_info2+ frameshift_info+ t_info+ a_info+ x1_info+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
x2_info+ x3_info+ s1_info+ s2_info
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx_ending"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx_ending</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
db_stats+ ungapped_lambda_stats+ matrix_stats+ generic_info1+ generic_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
info2+ frameshift_info+ t_info+ a_info+ x1_info+ x2_info+ s1_info+ s2_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
info
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="format"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">format</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.record(Group("appheader", NullOp())+ header+ Rep(hit)+ Group("endi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ng", NullOp()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastn_appheader), ("hsp_header"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, blastn_hsp_header), ("ending", blastn_ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastp_appheader), ("hsp_header"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, blastp_hsp_header), ("ending", blastp_ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastx_appheader), ("hsp_header"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, blastx_hsp_header), ("ending", blastx_ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", tblastn_appheader), ("hsp_header<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
", tblastn_hsp_header), ("ending", tblastn_ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", tblastx_appheader), ("hsp_header<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
", tblastx_hsp_header), ("ending", tblastx_ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="__warningregistry__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">__warningregistry__</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it does not work with recent ver</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">sions of mxTextTools. If you want to continue to use this module, plea</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">se get in contact with the Biopython developers at biopython-dev@biopy</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">thon.org to avoid permanent removal of this module from Biopython</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
2<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
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