/var/lib/mobyle/programs/wublast2.xml is in mobyle-programs 5.1.1-1.
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The actual contents of the file can be viewed below.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>wublast2</name>
<version>2.0</version>
<doc>
<title>WUBLAST2</title>
<description>
<text lang="en">Wash-U. BLAST, with gaps</text>
</description>
<authors>Gish. W</authors>
<reference>Gish, Warren (1994-1997). unpublished.</reference>
<reference>Gish, W, and DJ States (1993). Identification of protein coding regions by database similarity search. Nature Genetics 3:266-72.</reference>
<reference>Altschul, SF, and W Gish (1996). Local alignment statistics. ed. R. Doolittle. Methods in Enzymology 266:460-80.</reference>
<reference>Korf, I, and W Gish (2000). MPBLAST: improved BLAST performance with multiplexed queries. Bioinformatics in press.</reference>
<reference>Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-10.</reference>
<homepagelink>http://blast.wustl.edu/</homepagelink>
</doc>
<category>database:search:homology</category>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1" iscommand="1">
<name>wublast2</name>
<prompt lang="en">Blast program</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a program</label>
</velem>
<velem>
<value>blastn</value>
<label>Blastn (nucleotide query / nucleotide db)</label>
</velem>
<velem>
<value>blastp</value>
<label>Blastp (amino acid query / protein db)</label>
</velem>
<velem>
<value>blastx</value>
<label>Blastx (nucleotide query translated / protein db)</label>
</velem>
<velem>
<value>tblastn</value>
<label>tBlastn (protein query / translated nucleotide db)</label>
</velem>
<velem>
<value>tblastx</value>
<label>tBlastx (nucleotide query translated / translated nucleotide db)</label>
</velem>
</vlist>
<format>
<code proglang="perl">"$value"</code>
<code proglang="python">str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">The five BLAST programs described here perform the following tasks:</text>
<text lang="en">- blastp compares an amino acid query sequence against a protein sequence database;</text>
<text lang="en">- blastn compares a nucleotide query sequence against a nucleotide sequence database;</text>
<text lang="en">- blastx compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database;</text>
<text lang="en">- tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).</text>
<text lang="en">- tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.</text>
</comment>
</parameter>
<paragraph>
<name>db</name>
<prompt lang="en">Database</prompt>
<argpos>2</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>protein_db</name>
<prompt lang="en">Protein db</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^blast[px]$/</code>
<code proglang="python">wublast2 in [ "blastp", "blastx" ]</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/protdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<comment>
<text lang="en">Choose a protein db for blastp or blastx.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>nucleotid_db</name>
<prompt lang="en">Nucleotid db</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^(blastn|tblast[nx])$/)</code>
<code proglang="python">wublast2 in [ "blastn", "tblastn", "tblastx" ]</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/nucdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<comment>
<text lang="en">Choose a nucleotide db for blastn, tblastn or tblastx</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>query</name>
<prompt lang="en">Query Sequence</prompt>
<parameters>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>query_seq</name>
<prompt lang="en">Query</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $query_seq"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>nosegs</name>
<prompt lang="en">Do not segment the query sequence on hyphen (-) characters (-nosegs)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -nosegs" : ""</code>
<code proglang="python">( "" , " -nosegs" )[ value ]</code>
</format>
<argpos>5</argpos>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>compat</name>
<prompt lang="en">BLAST version</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>current</value>
</vdef>
<vlist>
<velem>
<value>current</value>
<label>Current version 2.0</label>
</velem>
<velem>
<value>compat1.4</value>
<label>BLAST version 1.4</label>
</velem>
<velem>
<value>compat1.3</value>
<label>BLAST version 1.3</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>5</argpos>
</parameter>
<paragraph>
<name>scoring_opt</name>
<prompt lang="en">Scoring options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>open_a_gap</name>
<prompt lang="en">Open gap penalty (Q)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "Q=$value" : "" </code>
<code proglang="python">( "" , " Q=" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default: 9 for proteins and 10 for nucleics.</text>
</comment>
<ctrl>
<message>
<text lang="en">requires an integral value in the range 1 <= Q < 2147483647</text>
</message>
<code proglang="perl">$value >= 1 and $value < 2147483647</code>
<code proglang="python">value >= 1 and value < 2147483647</code>
</ctrl>
</parameter>
<parameter>
<name>extend_a_gap</name>
<prompt lang="en">Extending a gap penalty (R)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " R=$value" : ""</code>
<code proglang="python">("" , " R=" + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default: 2 for proteins; 10 for nucleics.</text>
</comment>
<ctrl>
<message>
<text lang="en">requires an integral value in the range 0 <= R < 2147483647</text>
</message>
<code proglang="perl">$value >= 0 and $value < 2147483647</code>
<code proglang="python">value >= 0 and value < 2147483647</code>
</ctrl>
</parameter>
<paragraph>
<name>scoring_blast</name>
<prompt lang="en">Protein penalty (not for blastn)</prompt>
<precond>
<code proglang="perl">$wublast2 ne "blastn"</code>
<code proglang="python">wublast2 != "blastn"</code>
</precond>
<parameters>
<parameter>
<name>matrix</name>
<prompt lang="en">Similarity matrix (-matrix)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>BLOSUM62</value>
</vdef>
<vlist>
<velem>
<value>BLOSUM30</value>
<label>BLOSUM30</label>
</velem>
<velem>
<value>BLOSUM35</value>
<label>BLOSUM35</label>
</velem>
<velem>
<value>BLOSUM40</value>
<label>BLOSUM40</label>
</velem>
<velem>
<value>BLOSUM45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>BLOSUM50</value>
<label>BLOSUM50</label>
</velem>
<velem>
<value>BLOSUM55</value>
<label>BLOSUM55</label>
</velem>
<velem>
<value>BLOSUM60</value>
<label>BLOSUM60</label>
</velem>
<velem>
<value>BLOSUM62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>BLOSUM65</value>
<label>BLOSUM65</label>
</velem>
<velem>
<value>BLOSUM70</value>
<label>BLOSUM70</label>
</velem>
<velem>
<value>BLOSUM75</value>
<label>BLOSUM75</label>
</velem>
<velem>
<value>BLOSUM80</value>
<label>BLOSUM80</label>
</velem>
<velem>
<value>BLOSUM85</value>
<label>BLOSUM85</label>
</velem>
<velem>
<value>BLOSUM90</value>
<label>BLOSUM90</label>
</velem>
<velem>
<value>PAM10</value>
<label>PAM10</label>
</velem>
<velem>
<value>PAM20</value>
<label>PAM20</label>
</velem>
<velem>
<value>PAM30</value>
<label>PAM30</label>
</velem>
<velem>
<value>PAM40</value>
<label>PAM40</label>
</velem>
<velem>
<value>PAM50</value>
<label>PAM50</label>
</velem>
<velem>
<value>PAM60</value>
<label>PAM60</label>
</velem>
<velem>
<value>PAM70</value>
<label>PAM70</label>
</velem>
<velem>
<value>PAM80</value>
<label>PAM80</label>
</velem>
<velem>
<value>PAM90</value>
<label>PAM90</label>
</velem>
<velem>
<value>PAM100</value>
<label>PAM100</label>
</velem>
<velem>
<value>PAM110</value>
<label>PAM110</label>
</velem>
<velem>
<value>PAM120</value>
<label>PAM120</label>
</velem>
<velem>
<value>PAM130</value>
<label>PAM130</label>
</velem>
<velem>
<value>PAM140</value>
<label>PAM140</label>
</velem>
<velem>
<value>PAM150</value>
<label>PAM150</label>
</velem>
<velem>
<value>PAM160</value>
<label>PAM160</label>
</velem>
<velem>
<value>PAM170</value>
<label>PAM170</label>
</velem>
<velem>
<value>PAM180</value>
<label>PAM180</label>
</velem>
<velem>
<value>PAM190</value>
<label>PAM190</label>
</velem>
<velem>
<value>PAM200</value>
<label>PAM200</label>
</velem>
<velem>
<value>PAM210</value>
<label>PAM210</label>
</velem>
<velem>
<value>PAM220</value>
<label>PAM220</label>
</velem>
<velem>
<value>PAM230</value>
<label>PAM230</label>
</velem>
<velem>
<value>PAM240</value>
<label>PAM240</label>
</velem>
<velem>
<value>PAM250</value>
<label>PAM250</label>
</velem>
<velem>
<value>PAM260</value>
<label>PAM260</label>
</velem>
<velem>
<value>PAM270</value>
<label>PAM270</label>
</velem>
<velem>
<value>PAM280</value>
<label>PAM280</label>
</velem>
<velem>
<value>PAM290</value>
<label>PAM290</label>
</velem>
<velem>
<value>PAM300</value>
<label>PAM300</label>
</velem>
<velem>
<value>PAM310</value>
<label>PAM310</label>
</velem>
<velem>
<value>PAM320</value>
<label>PAM320</label>
</velem>
<velem>
<value>PAM330</value>
<label>PAM330</label>
</velem>
<velem>
<value>PAM340</value>
<label>PAM340</label>
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<velem>
<value>PAM350</value>
<label>PAM350</label>
</velem>
<velem>
<value>PAM360</value>
<label>PAM360</label>
</velem>
<velem>
<value>PAM370</value>
<label>PAM370</label>
</velem>
<velem>
<value>PAM380</value>
<label>PAM380</label>
</velem>
<velem>
<value>PAM390</value>
<label>PAM390</label>
</velem>
<velem>
<value>PAM400</value>
<label>PAM400</label>
</velem>
<velem>
<value>identity</value>
<label>Identity</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -matrix $value" : ""</code>
<code proglang="python">( "" , " -matrix " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Several PAM (point accepted mutations per 100 residues) amino acid scoring matrices are provided in the BLAST software distribution, including the PAM40, PAM120, and PAM250. While the BLOSUM62 matrix is a good general purpose scoring matrix and is the default matrix used by the BLAST programs, if one is restricted to using only PAM scoring matrices, then the PAM120 is recommended for general protein similarity searches (Altschul, 1991). The pam(1 program can be used to produce PAM matrices of any desired iteration from 2 to 511. Each matrix is most sensitive at finding similarities at its particular PAM distance. For more thorough searches, particularly when the mutational distance between potential homologs is unknown and the significance of their similarity may be only marginal, Altschul (1991, 1992) recommends performing at least three searches, one each with the PAM40, PAM120 and PAM250 matrices.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>scoring_blastn</name>
<prompt lang="en">Blastn penalty</prompt>
<precond>
<code proglang="perl">$wublast2 eq "blastn"</code>
<code proglang="python">wublast2 == "blastn"</code>
</precond>
<parameters>
<parameter>
<name>mismatch</name>
<prompt lang="en">Penalty for a nucleotid mismatch (N)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 eq blastn</code>
<code proglang="python">wublast2 == "blastn"</code>
</precond>
<vdef>
<value>-4</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " N=$value" : ""</code>
<code proglang="python">( "" , " N=" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>match</name>
<prompt lang="en">Reward for a nucleotid match (M)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " M=$value" : ""</code>
<code proglang="python">( "" , " M=" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>filter_opt</name>
<prompt lang="en">Filtering and masking options</prompt>
<argpos>6</argpos>
<parameters>
<parameter>
<name>filter</name>
<prompt lang="en">Filter or Masking query sequence</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>No filter</label>
</velem>
<velem>
<value>filter</value>
<label>Filter</label>
</velem>
<velem>
<value>wordmask</value>
<label>Masking</label>
</velem>
</vlist>
<comment>
<text lang="en">Mask letters in the query sequence without altering the sequence itself, during neighborhood word generation.</text>
</comment>
</parameter>
<parameter>
<name>other_filters</name>
<prompt lang="en">Filtering or Masking options</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined($filter)</code>
<code proglang="python">filter is not None</code>
</precond>
<vdef>
<value>seg</value>
</vdef>
<vlist>
<velem>
<value>dust</value>
<label>DNA filter (-dust)</label>
</velem>
<velem>
<value>seg</value>
<label>Masks low compositional complexity regions (-seg)</label>
</velem>
<velem>
<value>xnu</value>
<label>Masks regions containing short-periodicity internal repeats (xnu)</label>
</velem>
<velem>
<value>seg+xnu</value>
<label>seg+xnu</label>
</velem>
</vlist>
<format>
<code proglang="perl">" -$filter $value"</code>
<code proglang="python">" -" + str(filter) + " " + str(value)</code>
</format>
<comment>
<text lang="en">This option activates filtering or masking of segments of the query sequence based on a potentially wide variety of criteria. The usual intent of filtering is to mask regions that are non-specific for protein identification using sequence similarity. For instance, it may be desired to mask acidic or basic segments that would otherwise yield overwhelming amounts of uninteresting, non-specific matches against a wide array of protein families from a comprehensive database search. The BLAST programs have internally-coded knowledge of the specific command line options needed to invoke the SEG and XNU programs as query sequence filters, but these two filter programs are not included in the BLAST software distribution and must be independently installed.</text>
<text lang="en">The SEG program (Wootton and Federhen, 1993) masks low compositional complexity regions, while XNU (Claverie and States, 1993) masks regions containing short-periodicity internal repeats. The BLAST programs can pipe the filtered output from one program into another. For instance, XNU+SEG or SEG+XNU can be specified as the filtermethod to have each program filter the query sequence in succession. Note that neither SEG nor XNU is suitable for filtering untranslated nucleotide sequences for use by blastn</text>
</comment>
</parameter>
<parameter>
<name>maskextra</name>
<prompt lang="en">Extend masking additional distance into flanking regions (-maskextra)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$filter eq "wordmask"</code>
<code proglang="python">filter == "wordmask" </code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -maskextra" : ""</code>
<code proglang="python">( "" , " -maskextra" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>lc</name>
<prompt lang="en">Filter lower-case letters in query</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>None</label>
</velem>
<velem>
<value>lcfilter</value>
<label>Filter by replacing with the appropriate ambiguity code (-lcfilter)</label>
</velem>
<velem>
<value>lcmask</value>
<label>Mask without altering the sequence (-lcfilter)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>selectivite</name>
<prompt lang="en">Selectivity Options</prompt>
<argpos>7</argpos>
<parameters>
<parameter issimple="1">
<name>Expect</name>
<prompt lang="en">Expected value (E)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>10.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " E=$value" : ""</code>
<code proglang="python">( "" , " E=" + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">The parameter Expect (E) establishes a statistical significance threshold for reporting database sequence matches. E is interpreted as the upper bound on the expected frequency of chance occurrence of an HSP (or set of HSPs) within the context of the entire database search. Any database sequence whose matching satisfies E is subject to being reported in the program output. If the query sequence and database sequences follow the random sequence model of Karlin and Altschul (1990), and if sufficiently sensitive BLAST algorithm parameters are used, then E may be thought of as the number of matches one expects to observe by chance alone during the database search. The default value for E is 10, while the permitted range for this Real valued parameter is 0 < E <= 1000.</text>
</comment>
</parameter>
<parameter>
<name>hspmax</name>
<prompt lang="en">Maximal number of HSPs saved or reported per subject sequence (-hspmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1000</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -hspmax $value" : ""</code>
<code proglang="python">( "" , " -hspmax " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>E2</name>
<prompt lang="en">Expected number of HSPs that will be found when comparing two sequences that each have the same length (E2)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " E2=$value" : ""</code>
<code proglang="python">("" , " E2=" + str(value))[ value is not None ]</code>
</format>
<comment>
<text lang="en">E2 is interpreted as the expected number of HSPs that will be found when comparing two sequences that each have the same length -- either 300 amino acids or 1000 nucleotides, whichever is appropriate for the particular program being used.</text>
<text lang="en">The default value for E2 is typically about 0.15 but may vary from version to version of each program.</text>
</comment>
</parameter>
<parameter>
<name>Cutoff</name>
<prompt lang="en">Cutoff score: threshold for report (S)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " S=$value" : ""</code>
<code proglang="python">( "" , " S=" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">The parameter Cutoff (S) represents the score at which a single HSP would by itself satisfy the significance threshold E. Higher scores -- higher values for S -- correspond to increasing statistical significance (lower probability of chance occurrence). Unless S is explicitly set on the command line, its default value is calculated from the value of E. If both S and E are set on the command line, the one which is the most restrictive is used. When neither parameter is specified on the command line, the default value for E is used to calculate S.</text>
</comment>
</parameter>
<parameter>
<name>S2</name>
<prompt lang="en">Cutoff score which defines HSPs (S2)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " S2=$value" : ""</code>
<code proglang="python">( "" , " S2=" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">S2 may be thought of as the score expected for the MSP between two sequences that each have the same length -- either 300 amino acids or 1000 nucleotides, whichever is appropriate for the particular program being used.</text>
<text lang="en">The default value for S2 will be calculated from E2 and, like the relationship between E and S, is dependent on the residue composition of the query sequence and the scoring system employed, as conveyed by the Karlin-Altschul K and Lambda statistics.</text>
</comment>
</parameter>
<parameter>
<name>W</name>
<prompt lang="en">Length of words identified in the query sequence (W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " W=$value" : ""</code>
<code proglang="python">( "" , " W=" + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">The task of finding HSPs begins with identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.</text>
</comment>
</parameter>
<parameter>
<name>T</name>
<prompt lang="en">Neighborhood word score threshold (T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " T=$value" : ""</code>
<code proglang="python">( "" , " T=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>nwstart</name>
<prompt lang="en">Start generating neighborhood words here in query (blastp/blastx) (-nwstart)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^blast[px]$/</code>
<code proglang="python">wublast2 in [ "blastp", "blastx" ]</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -nwstart $value" : ""</code>
<code proglang="python">( "" , " -nwstart " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Restrict blast neighborhood word generation to a specific segment of the query sequence that begins at 'nwstart' and continues for 'nwlen' residues or until the end of the query sequence is reached. HSP alignments may extend outside the region of neighborhood word generation but hte alignments can only be initiated by word hits occurring within the region. Through the use of these options, a very long query sequence can be searched piecemeal, using short, overlapping segments each time. The amount of overlap from one neighborhood region to the next need only be the blast wordlength W minus 1, in order to be assured of detecting all HSPs.</text>
<text lang="en">However, to provide greater freedom for statistical interpretation of multiple HSP findings (eg. matches against exons) more extensive overlapping is recommanded, with the extent to be chosen based on the expected gene density and length of introns.</text>
</comment>
</parameter>
<parameter>
<name>nwlen</name>
<prompt lang="en">Generate neighborhood words over this distance from 'nwstart' in query (blastp/blastx) (-nwlen)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^blast[px]$/</code>
<code proglang="python">wublast2 in [ "blastp", "blastx" ]</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -nwlen $value" : ""</code>
<code proglang="python">( "" , " -nwlen " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>X</name>
<prompt lang="en">Word hit extension drop-off score (X)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " X=$value" : ""</code>
<code proglang="python">( "" , " X=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>hitdist</name>
<prompt lang="en">Maximum word separation distance for 2-hit BLAST algorithm (-hitdist)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -hitdist $value" : ""</code>
<code proglang="python">( "" , " -hitdist " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Invoke a 2-hit BLAST algorithm similar to that of Altschul et al. (1997), with maximum wordhit separation distance, as measured from the end of each wordhit. Altschul et al. (1997) use the equivalent of hitdist=40 in their software by default (except NCBI-BLASTN, where 2-hit BLAST is not available). In WU-BLASTN, setting 'hitdist' and 'wink' (see below) is akin to using double-length words generated on W-mer boundaries.</text>
<text lang="en">For best sensitivity, 2-hit BLAST should generally not be used.</text>
</comment>
</parameter>
<parameter>
<name>wink</name>
<prompt lang="en">Generate word hits at every wink-th position (-wink)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -wink $value" : ""</code>
<code proglang="python">( "" , " -wink " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Generate word hits at every wink-th ('W increment') position along the query, where the default wink=1 produces neighborhood words at every position.</text>
<text lang="en">For good sensitivity, this option should not be used. The benefit of using 'wink' is in finding identical or nearly identical sequences rapidly. When used in conjunction with the 'hitdist' option to obtain the highest speed, care should be taken that desired matches are not precluded by these parameters.</text>
</comment>
</parameter>
<parameter>
<name>consistency</name>
<prompt lang="en">Turn off HSP consistency rules for statistics (-consistency)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -consistency" : ""</code>
<code proglang="python">( "" , " -consistency" )[ value ]</code>
</format>
<comment>
<text lang="en">This option turns off both the determination of the number of HSPs that ar consistent with each other in a gapped alignment and an adjustment that is made to the Sum and poisson statistics to account for the consistency of combined HSPs.</text>
</comment>
</parameter>
<parameter>
<name>hspsepqmax</name>
<prompt lang="en">Maximal separation allowed between HSPs along query (-hspsepqmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $consistency</code>
<code proglang="python">not consistency</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -hspsepqmax $value" : ""</code>
<code proglang="python">( "" , " -hspsepqmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>hspsepsmax</name>
<prompt lang="en">Maximal separation allowed between HSPs along subject (-hspsepsmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $consistency</code>
<code proglang="python">not consistency </code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -hspsepsmax $value" : ""</code>
<code proglang="python">( "" , " -hspsepsmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>span</name>
<prompt lang="en">Discard HSPs spanned on (-span*)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>span2</value>
</vdef>
<vlist>
<velem>
<value>span2</value>
<label>Both query and subject by a better HSP (span2)</label>
</velem>
<velem>
<value>span1</value>
<label>On query, subject or both by a better HSP (span1)</label>
</velem>
<velem>
<value>span</value>
<label>By other, better HSPs (span)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>nogap</name>
<prompt lang="en">Do not create gapped alignments (-nogap)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -nogap" : ""</code>
<code proglang="python">( "" , " -nogap" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>gapall</name>
<prompt lang="en">Generate a gapped alignment for every ungapped HSP found (-gapall)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -gapall" : ""</code>
<code proglang="python">( "" , " -gapall" )[ value ]</code>
</format>
</parameter>
<paragraph>
<name>gap_selectivite</name>
<prompt lang="en">Selectivity options for gapped alignments</prompt>
<precond>
<code proglang="perl">not $nogap and not $gapall </code>
<code proglang="python">not nogap and not gapall </code>
</precond>
<argpos>5</argpos>
<parameters>
<parameter>
<name>gapE</name>
<prompt lang="en">Expectation threshold of sets of ungapped HSPs for subsequent use in seeding gapped alignments (-gapE)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>2000</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -gapE $value" : ""</code>
<code proglang="python">( "" , " -gapE " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>gapE2</name>
<prompt lang="en">Expectation threshold for saving individual gapped alignments (-gapE2)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -gapE2 $value" : ""</code>
<code proglang="python">( "" , " -gapE2 " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapS2</name>
<prompt lang="en">Cutoff score for saving individual gapped alignments (-gapS2)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -gapS2 $value" : ""</code>
<code proglang="python">( "" , " -gapS2 " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapW</name>
<prompt lang="en">Set the window width within which gapped alignments are generated (-gapW)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -gapW $value" : ""</code>
<code proglang="python">( "" , " -gapW " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Default values are 32 for protein comparisons and 16 for blastn.</text>
</comment>
</parameter>
<parameter>
<name>gapX</name>
<prompt lang="en">Set the maximum drop-off score during banded gapped alignment (gapX)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " gapX=$value" : ""</code>
<code proglang="python">("" , " gapX=" + str(value))[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapsepqmax</name>
<prompt lang="en">Maximal permitted distance on the QUERY sequence between two consistent gapped alignments (-gapsepqmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $nogap and not $consistency </code>
<code proglang="python">not nogap and not consistency </code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -gapsepqmax $value" : ""</code>
<code proglang="python">( "" , " -gapsepqmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapsepsmax</name>
<prompt lang="en">Maximal permitted distance on the subject sequence between two consistent gapped alignments (-gapsepsmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $nogap and not $consistency</code>
<code proglang="python">not nogap and not consistency </code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -gapsepsmax $value" : ""</code>
<code proglang="python">( "" , " -gapsepsmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>translation_opt</name>
<prompt lang="en">Translation Option</prompt>
<precond>
<code proglang="perl">$wublast2 ne blastn</code>
<code proglang="python">wublast2 != "blastn"</code>
</precond>
<argpos>6</argpos>
<parameters>
<parameter>
<name>gcode</name>
<prompt lang="en">Genetic code to translate the query (blastx,tblastx) (-gcode)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^t?blastx$/</code>
<code proglang="python">wublast2 in [ "blastx" , "tblastx" ]</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Standard (1)</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate Mitochondrial (2)</label>
</velem>
<velem>
<value>3</value>
<label>Yeast Mitochondrial (3)</label>
</velem>
<velem>
<value>4</value>
<label>Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma (4)</label>
</velem>
<velem>
<value>5</value>
<label>Invertebrate Mitochondrial (5)</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate Macronuclear and Dasycladacean (6)</label>
</velem>
<velem>
<value>9</value>
<label>Echinoderm Mitochondrial (9)</label>
</velem>
<velem>
<value>10</value>
<label>Alternative Ciliate Macronuclear (10)</label>
</velem>
<velem>
<value>11</value>
<label>Bacterial (11)</label>
</velem>
<velem>
<value>12</value>
<label>Alternative Yeast Nuclear (12)</label>
</velem>
<velem>
<value>13</value>
<label>Ascidian Mitochondrial (13)</label>
</velem>
<velem>
<value>14</value>
<label>Flatworm Mitochondrial (14)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -gcode $value" : ""</code>
<code proglang="python">( "" , " -gcode " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>strand</name>
<prompt lang="en">Which strands (for nucleotid query)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^blast[nx]$/</code>
<code proglang="python">wublast2 in [ "blastn", "blastx" ]</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Both</label>
</velem>
<velem>
<value>-top</value>
<label>Top</label>
</velem>
<velem>
<value>-bottom</value>
<label>Bottom</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[value is not None] </code>
</format>
</parameter>
<parameter>
<name>dbgcode</name>
<prompt lang="en">Genetic code for database translation (tblastx,tblastn) (-dbgcode)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^tblast[nx]$/</code>
<code proglang="python">wublast2 in [ "tblastx", "tblastn" ]</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Standard (1)</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate Mitochondrial (2)</label>
</velem>
<velem>
<value>3</value>
<label>Yeast Mitochondrial (3)</label>
</velem>
<velem>
<value>4</value>
<label>Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma (4)</label>
</velem>
<velem>
<value>5</value>
<label>Invertebrate Mitochondrial (5)</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate Macronuclear and Dasycladacean (6)</label>
</velem>
<velem>
<value>9</value>
<label>Echinoderm Mitochondrial (9)</label>
</velem>
<velem>
<value>10</value>
<label>Alternative Ciliate Macronuclear (10)</label>
</velem>
<velem>
<value>11</value>
<label>Bacterial (11)</label>
</velem>
<velem>
<value>12</value>
<label>Alternative Yeast Nuclear (12)</label>
</velem>
<velem>
<value>13</value>
<label>Ascidian Mitochondrial (13)</label>
</velem>
<velem>
<value>14</value>
<label>Flatworm Mitochondrial (14)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? "-dbgcode $value" : ""</code>
<code proglang="python">( "" , "-dbgcode " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>dbstrand</name>
<prompt lang="en">Which strands of the database sequences (tblastn,tblastx) (-db)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 =~ /^tblast[nx]$/</code>
<code proglang="python">wublast2 in [ "tblastn" , "tblastx" ]</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>Both</label>
</velem>
<velem>
<value>-dbtop</value>
<label>Top</label>
</velem>
<velem>
<value>-dbbottom</value>
<label>Bottom</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>statistics</name>
<prompt lang="en">Statistic options</prompt>
<argpos>6</argpos>
<comment>
<text lang="en">Parameters to use when evaluating the significance of gapped and ungapped alignment scores. Useful when precomputed values are unavailable for the chosen scoring matrix and gap penalty combination in the programs internal tables.</text>
</comment>
<parameters>
<parameter>
<name>stat</name>
<prompt lang="en">Use statistics</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>sump</value>
</vdef>
<vlist>
<velem>
<value>poissonp</value>
<label>Poisson statistics to evaluate multiple HSPs (poissonp)</label>
</velem>
<velem>
<value>kap</value>
<label>Karlin-Altschul statistics on individual alignment scores (kap)</label>
</velem>
<velem>
<value>sump</value>
<label>Karlin-Altschul 'Sum' statistics (sump)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>wordstats</name>
<prompt lang="en">Collect word-hit statistics (-stats)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -stats" : ""</code>
<code proglang="python">( "" , " -stats" )[ value ]</code>
</format>
<comment>
<text lang="en">This option consumes marginally more cpu time.</text>
</comment>
</parameter>
<parameter>
<name>ctxfactor</name>
<prompt lang="en">Base statistics on this number of independent contexts or reading frames (-ctxfactor)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -ctxfactor $value" : ""</code>
<code proglang="python">( "" , " -ctxfactor " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>olf</name>
<prompt lang="en">Maximal fractional length of overlap for HSP consistency of two ungapped alignment (-olf)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.125</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -olf $value" : ""</code>
<code proglang="python">( "" , " -olf " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en"/>
</comment>
</parameter>
<parameter>
<name>golf</name>
<prompt lang="en">Maximal fractional length of overlap for HSP consistency of two gapped alignments (-golf)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -golf $value" : ""</code>
<code proglang="python">( "" , " -golf " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>olmax</name>
<prompt lang="en">Maximal absolute length of overlap for HSP consistency of two ungapped alignment (default unlimited) (-olmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -olmax $value" : ""</code>
<code proglang="python">( "" , " -olmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>golmax</name>
<prompt lang="en">Maximal absolute length of overlap for HSP consistency of two gapped alignment (default unlimited) (-golmax)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -golmax $value" : ""</code>
<code proglang="python">( "" , " -golmax " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapdecayrate</name>
<prompt lang="en">Gap decay rate (-gapdecayrate)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -gapdecayrate $value" : ""</code>
<code proglang="python">( "" , " -gapdecayrate " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">This option defines the common ratio of the terms in a geometric progression used in normalizing probabilities across all numbers of Poisson events (typically the number of 'consistent' HSPs). A Poisson probability for N segments is eighted by the reciprocal of the Nth term in the progression, where the first term has a value of (1-rate), the second term is (1-rate)*rate, the third term is (1-rate)*rate*rate, and so on.</text>
<text lang="en">The default rate is 0.5, such that the probability assigned to a single HSP is discounted by a factor of 2, the Poisson probability of 2 HSPs is discounted by a factor of 4, for 3 HSPs the discount factor is 8, and so on. The rate essentially defines a penalty imposed on the gap between each HSP, where the default penalty is equivalent to 1 bit of information.</text>
</comment>
</parameter>
<paragraph>
<name>kastats</name>
<prompt lang="en">Parameters for Karlin-Altschul statistics</prompt>
<precond>
<code proglang="perl">$stat =~ /^(kap|sump)$/</code>
<code proglang="python">stat in [ "kap", "sump" ]</code>
</precond>
<argpos>6</argpos>
<parameters>
<parameter>
<name>K</name>
<prompt lang="en">K parameter for ungapped alignment scores (K)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " K=$value" : ""</code>
<code proglang="python">( "" , " K=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>L</name>
<prompt lang="en">Lambda parameter for ungapped alignment scores (L)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " L=$value" : ""</code>
<code proglang="python">( "" , " L=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>H</name>
<prompt lang="en">H parameter for ungapped alignment scores (H)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " H=$value" : ""</code>
<code proglang="python">( "" , " H=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapK</name>
<prompt lang="en">K parameter for gapped alignment scores (gapK)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " gapK=$value" : ""</code>
<code proglang="python">( "" , " gapK=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapL</name>
<prompt lang="en">Lambda parameter for gapped alignment scores (gapL)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " gapL=$value" : ""</code>
<code proglang="python">( "" , " gapL=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gapH</name>
<prompt lang="en">H parameter for gapped alignment scores (gapH)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " gapH=$value" : ""</code>
<code proglang="python">( "" , " gapH=" + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>affichage</name>
<prompt lang="en">Report options</prompt>
<argpos>5</argpos>
<parameters>
<parameter>
<name>Histogram</name>
<prompt lang="en">Histogram (H)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " H=1" : ""</code>
<code proglang="python">( "" , " H=1" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>Descriptions</name>
<prompt lang="en">How many short descriptions? (V)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>500</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " V=$value" : ""</code>
<code proglang="python">( "" , " V=" + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Maximum number of database sequences for which one-line descriptions will be reported (V).</text>
</comment>
</parameter>
<parameter>
<name>Alignments</name>
<prompt lang="en">How many alignments? (B)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>250</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " B=$value" : ""</code>
<code proglang="python">( "" , " B=" + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Maximum number of database sequences for which high-scoring segment pairs will be reported (B).</text>
</comment>
</parameter>
<parameter>
<name>sortby</name>
<prompt lang="en">Sort order for reporting database sequences</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>sort_by_pvalue</value>
</vdef>
<vlist>
<velem>
<value>sort_by_pvalue</value>
<label>From most significant to least significant (sort_by_pvalue)</label>
</velem>
<velem>
<value>sort_by_count</value>
<label>From highest to lowest by the number of HSPs found (sort_by_count)</label>
</velem>
<velem>
<value>sort_by_highscore</value>
<label>From highest to lowest by the score of the highest segment (sort_by_highscore)</label>
</velem>
<velem>
<value>sort_by_totalscore</value>
<label>From highest to the lowest by the sum total score (sort_by_totalscore)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>postsw</name>
<prompt lang="en">Perform full Smith-Waterman before output (blastp only) (-postsw)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$wublast2 eq "blastp"</code>
<code proglang="python">wublast2 == "blastp"</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -postsw" : ""</code>
<code proglang="python">( "" , " -postsw" )[ value ]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>output_file</name>
<prompt lang="en">Output file name</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -o blast.txt"</code>
<code proglang="python">" -o blast.txt"</code>
</format>
<argpos>499</argpos>
</parameter>
<parameter ishidden="1">
<!-- We limit the number of CPUs to use to run the job, otherwise
wublast will use all the available CPUs automatically -->
<name>cpunum</name>
<prompt lang="en">CPU number to use</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -cpus 1"</code>
<code proglang="python">" -cpus 1"</code>
</format>
<argpos>499</argpos>
</parameter>
<parameter>
<name>output_format</name>
<prompt lang="en">Html output format</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">" && html4blast -g -o blast.html blast.txt"</code>
<code proglang="python">("" , " && html4blast -g -o blast.html blast.txt")[ value ] </code>
</format>
<argpos>500</argpos>
</parameter>
<parameter>
<name>echofilter</name>
<prompt lang="en">Display filter sequences in output (-echofilter)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -echofilter" : ""</code>
<code proglang="python">( "" , " -echofilter" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>prune</name>
<prompt lang="en">Do not prune insignificant HSPs from the output lists (-prune)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -prune" : ""</code>
<code proglang="python">( "" , " -prune" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>topcomboN</name>
<prompt lang="en">Report this number of consistent (colinear) groups of HSPs (-topcomboN)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -topcomboN $value" : ""</code>
<code proglang="python">( "" , " -topcomboN " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>topcomboE</name>
<prompt lang="en">Only show HSP combos within this factor of the best combo (-topcomboE)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -topcomboE $value" : ""</code>
<code proglang="python">( "" , " -topcomboE " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>gi</name>
<prompt lang="en">Display gi identifiers, when available (-gi)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -gi" : ""</code>
<code proglang="python">( "" , " -gi" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>noseqs</name>
<prompt lang="en">Do not display sequence alignments (-noseqs)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -noseqs" : ""</code>
<code proglang="python">( "" , " -noseqs" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>tmp_outfile</name>
<prompt lang="en">Blast report</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"blast.txt"</code>
<code proglang="python">"blast.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>htmlfile</name>
<prompt lang="en">Blast html report</prompt>
<type>
<datatype>
<class>BlastHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"blast.html"</code>
<code proglang="python">"blast.html"</code>
</filenames>
</parameter>
<parameter isout="1" ishidden="1">
<name>imgfile</name>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.png"</code>
<code proglang="perl">"*.gif"</code>
<code proglang="python">"*.png"</code>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xmloutput</name>
<prompt lang="en">Blast xml report</prompt>
<type>
<datatype>
<class>BlastXmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"blast.xml"</code>
<code proglang="python">"blast.xml"</code>
</filenames>
</parameter>
</parameters>
</program>
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