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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11">
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2 <description>Search nucleotide database with nucleotide query sequence(s)</description>
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3 <version_command>blastn -version</version_command>
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4 <command interpreter="python">hide_stderr.py
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5 ## The command is a Cheetah template which allows some Python based syntax.
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6 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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7 blastn
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8 -query "$query"
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9 #if $db_opts.db_opts_selector == "db":
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10 -db "${db_opts.database.fields.path}"
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11 #else:
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12 -subject "$db_opts.subject"
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13 #end if
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14 -task $blast_type
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15 -evalue $evalue_cutoff
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16 -out $output1
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17 ##Set the extended list here so if/when we add things, saved workflows are not affected
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18 #if str($out_format)=="ext":
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19 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
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20 #else:
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21 -outfmt $out_format
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22 #end if
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23 -num_threads 8
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24 #if $adv_opts.adv_opts_selector=="advanced":
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25 $adv_opts.filter_query
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26 $adv_opts.strand
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27 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
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28 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
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29 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
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30 -max_target_seqs $adv_opts.max_hits
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31 #end if
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32 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
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33 -word_size $adv_opts.word_size
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34 #end if
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35 $adv_opts.ungapped
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36 $adv_opts.parse_deflines
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37 ## End of advanced options:
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38 #end if
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39 </command>
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40 <inputs>
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41 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
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42 <conditional name="db_opts">
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43 <param name="db_opts_selector" type="select" label="Subject database/sequences">
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44 <option value="db" selected="True">BLAST Database</option>
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45 <option value="file">FASTA file</option>
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46 </param>
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47 <when value="db">
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48 <param name="database" type="select" label="Nucleotide BLAST database">
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49 <options from_file="blastdb.loc">
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50 <column name="value" index="0"/>
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51 <column name="name" index="1"/>
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52 <column name="path" index="2"/>
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53 </options>
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54 </param>
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55 <param name="subject" type="hidden" value="" />
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56 </when>
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57 <when value="file">
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58 <param name="database" type="hidden" value="" />
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59 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
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60 </when>
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61 </conditional>
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62 <param name="blast_type" type="select" display="radio" label="Type of BLAST">
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63 <option value="megablast">megablast</option>
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64 <option value="blastn">blastn</option>
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65 <option value="blastn-short">blastn-short</option>
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66 <option value="dc-megablast">dc-megablast</option>
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67 <!-- Using BLAST 2.2.24+ this gives an error:
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68 BLAST engine error: Program type 'vecscreen' not supported
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69 <option value="vecscreen">vecscreen</option>
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70 -->
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71 </param>
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72 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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73 <param name="out_format" type="select" label="Output format">
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74 <option value="6" selected="True">Tabular (standard 12 columns)</option>
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75 <option value="ext">Tabular (extended 24 columns)</option>
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76 <option value="5">BLAST XML</option>
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77 <option value="0">Pairwise text</option>
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78 <option value="0 -html">Pairwise HTML</option>
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79 <option value="2">Query-anchored text</option>
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80 <option value="2 -html">Query-anchored HTML</option>
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81 <option value="4">Flat query-anchored text</option>
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82 <option value="4 -html">Flat query-anchored HTML</option>
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83 <!--
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84 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
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85 -->
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86 </param>
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87 <conditional name="adv_opts">
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88 <param name="adv_opts_selector" type="select" label="Advanced Options">
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89 <option value="basic" selected="True">Hide Advanced Options</option>
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90 <option value="advanced">Show Advanced Options</option>
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91 </param>
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92 <when value="basic" />
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93 <when value="advanced">
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94 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
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95 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
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96 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
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97 <option value="-strand both">Both</option>
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98 <option value="-strand plus">Plus (forward)</option>
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99 <option value="-strand minus">Minus (reverse complement)</option>
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100 </param>
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101 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
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102 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
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103 <validator type="in_range" min="0" />
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104 </param>
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105 <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
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106 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
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107 <validator type="in_range" min="0" />
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108 </param>
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109 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
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110 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
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111 </when>
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112 </conditional>
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113 </inputs>
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114 <outputs>
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115 <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
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116 <change_format>
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117 <when input="out_format" value="0" format="txt"/>
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118 <when input="out_format" value="0 -html" format="html"/>
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119 <when input="out_format" value="2" format="txt"/>
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120 <when input="out_format" value="2 -html" format="html"/>
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121 <when input="out_format" value="4" format="txt"/>
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122 <when input="out_format" value="4 -html" format="html"/>
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123 <when input="out_format" value="5" format="blastxml"/>
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124 </change_format>
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125 </data>
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126 </outputs>
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127 <requirements>
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128 <requirement type="binary">blastn</requirement>
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129 </requirements>
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130 <help>
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131
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132 .. class:: warningmark
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133
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134 **Note**. Database searches may take a substantial amount of time.
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135 For large input datasets it is advisable to allow overnight processing.
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136
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137 -----
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138
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139 **What it does**
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140
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141 Search a *nucleotide database* using a *nucleotide query*,
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142 using the NCBI BLAST+ blastn command line tool.
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143 Algorithms include blastn, megablast, and discontiguous megablast.
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144
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145 -----
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146
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147 **Output format**
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148
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149 Because Galaxy focuses on processing tabular data, the default output of this
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150 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
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151
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152 ====== ========= ============================================
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153 Column NCBI name Description
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154 ------ --------- --------------------------------------------
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155 1 qseqid Query Seq-id (ID of your sequence)
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156 2 sseqid Subject Seq-id (ID of the database hit)
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157 3 pident Percentage of identical matches
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158 4 length Alignment length
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159 5 mismatch Number of mismatches
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160 6 gapopen Number of gap openings
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161 7 qstart Start of alignment in query
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162 8 qend End of alignment in query
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163 9 sstart Start of alignment in subject (database hit)
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164 10 send End of alignment in subject (database hit)
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165 11 evalue Expectation value (E-value)
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166 12 bitscore Bit score
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167 ====== ========= ============================================
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168
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169 The BLAST+ tools can optionally output additional columns of information,
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170 but this takes longer to calculate. Most (but not all) of these columns are
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171 included by selecting the extended tabular output. The extra columns are
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172 included *after* the standard 12 columns. This is so that you can write
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173 workflow filtering steps that accept either the 12 or 24 column tabular
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174 BLAST output.
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175
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176 ====== ============= ===========================================
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177 Column NCBI name Description
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178 ------ ------------- -------------------------------------------
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179 13 sallseqid All subject Seq-id(s), separated by a ';'
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180 14 score Raw score
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181 15 nident Number of identical matches
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182 16 positive Number of positive-scoring matches
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183 17 gaps Total number of gaps
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184 18 ppos Percentage of positive-scoring matches
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185 19 qframe Query frame
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186 20 sframe Subject frame
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187 21 qseq Aligned part of query sequence
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188 22 sseq Aligned part of subject sequence
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189 23 qlen Query sequence length
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190 24 slen Subject sequence length
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191 ====== ============= ===========================================
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192
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193 The third option is BLAST XML output, which is designed to be parsed by
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194 another program, and is understood by some Galaxy tools.
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195
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196 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
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197 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
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198 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
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199 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
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200 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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201
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202 -------
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203
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204 **References**
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205
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206 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
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207
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208 </help>
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209 </tool>
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