/var/lib/mobyle/programs/bl2seq.xml is in mobyle-programs 5.1.2-2.
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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>bl2seq</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/blast_package.xml"/>
<doc>
<title>BL2SEQ</title>
<description>
<text lang="en">Comparison between two sequences with Blast (NCBI)</text>
</description>
</doc>
<category>alignment:pairwise</category>
</head>
<parameters>
<parameter ishidden="1" iscommand="1">
<name>blast_init</name>
<prompt lang="en">Blast initiation</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"bl2seq"</code>
<code proglang="python">"bl2seq"</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>bl2seq</name>
<prompt lang="en">Blast program (-p)</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>blastp</value>
<label>Blastp (protein/protein)</label>
</velem>
<velem>
<value>blastn</value>
<label>Blastn (nucleotide/nucleotide)</label>
</velem>
<velem>
<value>blastx</value>
<label>Blastx (translated nucleotide/ protein)</label>
</velem>
<velem>
<value>tblastn</value>
<label>tBlastn (protein/translated nucleotide)</label>
</velem>
<velem>
<value>tblastx</value>
<label>tBlastx (translated nucleotide/translated nucleotide)</label>
</velem>
</vlist>
<format>
<code proglang="perl">" -p $value"</code>
<code proglang="python">" -p " + str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">- Blastp compares amino acid query sequences</text>
<text lang="en">- Blastn compares nucleotide query sequences</text>
<text lang="en">- tBlastx compares translated a nucleotide sequence and an amino acid sequence</text>
<text lang="en">- tBlastn compares an amino acid sequence translated and a nucleotide sequence</text>
<text lang="en">- tBlastx compares translated nucleotide sequences</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>first_sequence</name>
<prompt lang="en">First sequence (-i)</prompt>
<type>
<biotype>Protein</biotype>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -i $value"</code>
<code proglang="python">" -i " + str( value )</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>first_start_region</name>
<prompt lang="en">Start of required region in first query sequence (-I)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<comment>
<text lang="en">Location on query sequence</text>
</comment>
</parameter>
<parameter>
<name>first_end_region</name>
<prompt lang="en">End of required region in first sequence (-I)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $first_start_region</code>
<code proglang="python">first_start_region is not None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -I \"$first_start_region $value\"" : " -I \"$first_start_region\""</code>
<code proglang="python">( ' -I "%s "' % (str(first_start_region)), ' -I "%s %s"' % (str(first_start_region), str(value)))[value is not None]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>second_sequence</name>
<prompt lang="en">Second sequence (-j)</prompt>
<type>
<biotype>Protein</biotype>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" -j $value"</code>
<code proglang="python">" -j " + str(value)</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter>
<name>second_start_region</name>
<prompt lang="en">Start of required region in second sequence (-J)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<argpos>4</argpos>
</parameter>
<parameter>
<name>second_end_region</name>
<prompt lang="en">End of required region in second sequence (-J)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $second_start_region</code>
<code proglang="python">second_start_region is not None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -J \"$second_start_region $value\"" : " -J \"$second_region\""</code>
<code proglang="python">( ' -J "%s "' % (str(second_start_region)), ' -J "%s %s"' % (str(second_start_region), str(value)))[value is not None]</code>
</format>
<argpos>4</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">Cost to open a gap (-G)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -G $value" : ""</code>
<code proglang="python">("" , " -G "+str(value) )[value is not None]</code>
</format>
<comment>
<text lang="en">Default: 5 for blastn; 10 for blastp, blastx and 11 for tblastn</text>
</comment>
</parameter>
<parameter>
<name>extend_a_gap</name>
<prompt lang="en">Cost to extend a gap (-E)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -E $value" : ""</code>
<code proglang="python">("" , " -E "+str(value) )[value is not None]</code>
</format>
<comment>
<text lang="en">Default: 2 for blastn; 1 for blastp, blastx and tblastn</text>
<text lang="en">Limited values for gap existence and extension are supported for these programs.</text>
<text lang="en">Existence -- Extension:</text>
<text lang="en">BLOSUM90</text>
<text lang="en">9 -- 2, 8 -- 2, 7 -- 2, 6 -- 2</text>
<text lang="en">11 -- 1, 10 -- 1, 9 -- 1</text>
<text lang="en">BLOSUM80</text>
<text lang="en">25 -- 2, 13 -- 2, 9 -- 2, 8 -- 2, 7 -- 2, 6 -- 2</text>
<text lang="en">11 -- 1, 10 -- 1, 9 -- 1</text>
<text lang="en">BLOSUM62</text>
<text lang="en">11 -- 2, 10 -- 2, 9 -- 2, 8 -- 2, 7 -- 2, 6 -- 2</text>
<text lang="en">13 -- 1, 12 -- 1, 11 -- 1, 10 -- 1, 9 -- 1</text>
<text lang="en">BLOSUM45</text>
<text lang="en">13 -- 3, 12 -- 3, 11 -- 3, 10 -- 3</text>
<text lang="en">16 -- 2, 15 -- 2, 14 -- 2, 13 -- 2, 12 -- 2</text>
<text lang="en">19 -- 1, 18 -- 1, 17 -- 1, 16 -- 1</text>
<text lang="en">PAM30</text>
<text lang="en">7 -- 2, 6 -- 2, 5 -- 2</text>
<text lang="en">10 -- 1, 9 -- 1, 8 -- 1</text>
<text lang="en">PAM70</text>
<text lang="en">8 -- 2, 7 -- 2, 6 -- 2</text>
<text lang="en">11 -- 1, 10 -- 1, 9 -- 1</text>
</comment>
</parameter>
<paragraph>
<name>scoring_blast</name>
<prompt lang="en">Protein penalty (not for blastn)</prompt>
<precond>
<code proglang="perl">$bl2seq ne "blastn"</code>
<code proglang="python">bl2seq != "blastn"</code>
</precond>
<parameters>
<parameter>
<name>matrix</name>
<prompt lang="en">Similarity matrix (-M)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>BLOSUM62</value>
</vdef>
<vlist>
<velem>
<value>BLOSUM90</value>
<label>BLOSUM90</label>
</velem>
<velem>
<value>BLOSUM80</value>
<label>BLOSUM80</label>
</velem>
<velem>
<value>BLOSUM62</value>
<label>BLOSUM62</label>
</velem>
<velem>
<value>BLOSUM50</value>
<label>BLOSUM50</label>
</velem>
<velem>
<value>BLOSUM45</value>
<label>BLOSUM45</label>
</velem>
<velem>
<value>PAM30</value>
<label>PAM30</label>
</velem>
<velem>
<value>PAM70</value>
<label>PAM70</label>
</velem>
<velem>
<value>PAM250</value>
<label>PAM250</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -M $value" : ""</code>
<code proglang="python">("" , " -M "+str(value) )[value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>scoring_blastn</name>
<prompt lang="en">Blastn penalty</prompt>
<precond>
<code proglang="perl">$bl2seq eq "blastn"</code>
<code proglang="python">bl2seq == "blastn"</code>
</precond>
<parameters>
<parameter>
<name>mismatch</name>
<prompt lang="en">Penalty for a nucleotide mismatch (-q)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>-3</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -q $value" : ""</code>
<code proglang="python">("" , " -q "+str(value) )[value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>match</name>
<prompt lang="en">Reward for a nucleotide match (-r)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -r $value" : ""</code>
<code proglang="python">("" , " -r "+str(value) )[value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>filter_opt</name>
<prompt lang="en">Filtering and masking options</prompt>
<argpos>6</argpos>
<comment>
<text lang="en">
Mask off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query
sequence available for specific matching against database sequences.
</text>
<text lang="en">
Filtering is only applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs. It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered
query sequence should be suspect.
</text>
</comment>
<parameters>
<parameter>
<name>filter</name>
<prompt lang="en">Filter or Masking query sequence (DUST with blastn, SEG with others) (-F)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -F F"</code>
<code proglang="python">(" -F F" , "")[ value ]</code>
</format>
</parameter>
<parameter>
<name>other_filters</name>
<prompt lang="en">Filtering options (Filter must be true)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$filter and not defined $other_masking</code>
<code proglang="python">filter and other_masking is None</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<flist>
<felem undef="1">
<value>null</value>
<label/>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>coil</value>
<label>Coiled-coiled filter ("C")</label>
<code proglang="perl">" -F C"</code>
<code proglang="python">" -F C"</code>
</felem>
<felem>
<value>seg+coil</value>
<label>Both SEG and coiled-coiled filters ("C;S")</label>
<code proglang="perl">" -F \"C;S\""</code>
<code proglang="python">" -F \"C;S\""</code>
</felem>
<felem>
<value>dust</value>
<label>DUST filter for DNA ("D")</label>
<code proglang="perl">" -F D"</code>
<code proglang="python">" -F D"</code>
</felem>
</flist>
<comment>
<text lang="en">A coiled-coiled filter, based on the work of Lupas et al. (Science, vol 252, pp. 1162-4 (1991)) written by John Kuzio (Wilson et al., J Gen Virol, vol. 76, pp. 2923-32 (1995))</text>
</comment>
</parameter>
<parameter>
<name>other_masking</name>
<prompt lang="en">Masking options (Filter must be true)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$filter == 1 and not defined $other_filters</code>
<code proglang="python">filter == 1 and other_filters is None</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<flist>
<felem undef="1">
<value>null</value>
<label/>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>maskSEG</value>
<label>Masking with SEG should only be done during the building of initial words ("m S")</label>
<code proglang="perl">" -F \"m S\""</code>
<code proglang="python">" -F \"m S\""</code>
</felem>
<felem>
<value>maskCoil</value>
<label>Masking with coiled-coil should only be done during the building of initial words ("m D")</label>
<code proglang="perl">" -F \"m D\""</code>
<code proglang="python">" -F \"m D\""</code>
</felem>
<felem>
<value>maskDust</value>
<label>Masking with DUST should only be done during the building of initial words ("m C")</label>
<code proglang="perl">" -F \"m C\""</code>
<code proglang="python">" -F \"m C\""</code>
</felem>
<felem>
<value>lowerMask</value>
<label>Lower-case masking (-U must be true) ("m")</label>
<code proglang="perl">" -F m"</code>
<code proglang="python">" -F m"</code>
</felem>
</flist>
<ctrl>
<message>
<text lang="en">For Lower-case masking the lower case filtering must be select.</text>
</message>
<code proglang="perl">($value eq 'null' or $value eq 'maskSEG' or $value eq 'maskCoil' or $value eq 'maskDust']) or ($value eq 'lowerMask' and $lower_case)</code>
<code proglang="python">value in ['null', 'maskSEG', 'maskCoil', 'maskDust'] or (value == 'lowerMask' and lower_case)</code>
</ctrl>
<comment>
<text lang="en">A coiled-coiled filter, based on the work of Lupas et al. (Science, vol 252, pp. 1162-4 (1991)) written by John Kuzio (Wilson et al., J Gen Virol, vol. 76, pp. 2923-32 (1995)).</text>
<text lang="en">It is possible to specify that the masking should only be done during the process of building the initial words .</text>
<text lang="en">If the -U option (to mask any lower-case sequence in the input FASTA file) is used and one does not wish any other filtering, but does wish to mask when building the lookup tables then one should specify: -F 'm'</text>
</comment>
</parameter>
<parameter>
<name>lower_case</name>
<prompt lang="en">Use lower case filtering (-U)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -U T" : ""</code>
<code proglang="python">("", " -U T")[value]</code>
</format>
<comment>
<text lang="en">This option specifies that any lower-case letters in the input FASTA file should be masked.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>selectivity_opt</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</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 statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are
acceptable.
</text>
</comment>
</parameter>
<parameter>
<name>word_size</name>
<prompt lang="en">Word Size (-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">Use words of size N.</text>
<text lang="en">Zero invokes default behavior</text>
<text lang="en">Default values:</text>
<text lang="en">- 11 for blastn</text>
<text lang="en">- 3 for others</text>
</comment>
</parameter>
<parameter>
<name>dropoff_extent</name>
<prompt lang="en">X dropoff value for gapped alignment (-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>
<comment>
<text lang="en">This is the value that control the path graph region explored by Blast during a gapped extension (Xg in the NAR paper) (default for blastp is 15).</text>
<text lang="en">Default values:</text>
<text lang="en">- 30 for blastn</text>
<text lang="en">- 0 for tblastx</text>
<text lang="en">- 15 for others</text>
</comment>
</parameter>
<parameter>
<name>eff_len</name>
<prompt lang="en">Effective length of the search space (-Y)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) " -Y $value" : ""</code>
<code proglang="python">("" , " -Y "+str(value) )[value is not None]</code>
</format>
<comment>
<text lang="en">Use zero for the real size</text>
</comment>
</parameter>
<parameter>
<name>gapped_alig</name>
<prompt lang="en">Perform or not gapped alignment (not available with tblastx) (-g)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$bl2seq ne "tblastx"</code>
<code proglang="python">bl2seq != "tblastx"</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : " -g F "</code>
<code proglang="python">(" -g F " , "")[value]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>translation_opt</name>
<prompt lang="en">Translation options</prompt>
<precond>
<code proglang="perl">$bl2seq =~ /^(blastx|tblast[nx])$/</code>
<code proglang="python">bl2seq in [ "blastx", "tblastx", "tblastn" ]</code>
</precond>
<argpos>8</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>strand</name>
<prompt lang="en">Query strand to search against second sequence (for blastx, tblastx or tblastn) (-S)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>3</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Top (1)</label>
</velem>
<velem>
<value>2</value>
<label>Bottom (2)</label>
</velem>
<velem>
<value>3</value>
<label>Both (3)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -S $value" : ""</code>
<code proglang="python">( "" , " -S " + str(value) )[ value is not None and value!= vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_opt</name>
<prompt lang="en">Output options</prompt>
<argpos>10</argpos>
<parameters>
<parameter>
<name>outformat</name>
<prompt lang="en">Output format (-D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Traditional (0)</label>
</velem>
<velem>
<value>1</value>
<label>Tabulated (1)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? "" : "-D $value"</code>
<code proglang="python">( "" , " -D " + str( value ) )[ value is not None and value != vdef]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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