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date Fri, 10 May 2013 17:15:08 -0400
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1 <!--
2 # =====================================================
3 # $Id: ExtractPeptideSequenceContext.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractPeptideSequenceContext.xml $
5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $
6 # $LastChangedRevision: 90 $
7 # $LastChangedBy: pieter.neerincx@gmail.com $
8 # =====================================================
9 -->
10 <tool id="ExtractPeptideSequenceContext1" version="0.1" name="Extract Peptide Context">
11 <description>by mapping peptides back to proteins and extending them on both termini to include their sequence context.</description>
12 <command interpreter="perl">ExtractPeptideSequenceContext.pl --db $db --dbf FASTA --f $fragments --icol $icol --pcol $pcol $strip --pepo $pepo --n $n --c $c --pc '$pc' --ll WARN</command>
13 <inputs>
14 <param name="fragments" type="data" format="tabular" label="Peptide sequences and their protein's identifiers"
15 help="(in tab delimited format)"/>
16 <param name="icol" type="data_column" value="1" data_ref="fragments" label="Protein identifier column"/>
17 <param name="pcol" type="data_column" value="2" data_ref="fragments" label="Peptide sequence column"/>
18 <!--
19 <param name="icol" type="integer" value="1" label="Protein identifier column"/>
20 <param name="pcol" type="integer" value="2" label="Peptide sequence column"/>
21 -->
22 <param name="strip" type="select">
23 <label>Lowercase characters in the peptide sequences represent</label>
24 <option value="--s">Modifications</option>
25 <option value="">Amino acids</option>
26 </param>
27 <param name="db" type="data" format="fasta" label="Protein sequences"
28 help="(in FASTA format)"/>
29 <param name="n" type="integer" value="5" label="N-terminal sequence context length"/>
30 <param name="c" type="integer" value="5" label="C-terminal sequence context length"/>
31 <param name="pc" type="select" help="to fill positions in the sequence context when the protein was too short for a full length context.">
32 <label>Padding character</label>
33 <option value="-">dash</option>
34 <option value=" ">space</option>
35 <option value="">none</option>
36 </param>
37 </inputs>
38 <outputs>
39 <data name="pepo" format="tabular" label="Peptide sequence contexts for ${fragments.name}"/>
40 </outputs>
41 <!--
42 <tests>
43 <test>
44 <param name="input" value="*.fasta"/>
45 <param name="identifiers" value="*.txt"/>
46 <output name="output" file="*.fasta"/>
47 </test>
48 </tests>
49 -->
50 <help>
51
52 .. role:: raw-html(raw)
53 :format: html
54
55 .. class:: infomark
56
57 **What it does**
58
59 Map peptide sequences back to proteins and extend the peptides on both termini to include their sequence context.
60
61 :raw-html:`&lt;object data="static/images/nbic_gmr/ExtractPeptideSequenceContext.svg" type="image/svg+xml" width="100%"/&gt;`
62
63 ===================================================
64 *Peptide sequences and their protein's identifiers*
65 ===================================================
66
67 This file must contain at least peptides and accession numbers or IDs of the proteins the peptides were derived from. \
68 The data must be in TAB delimited format and may contain other columns, which will be preserved in the output. \
69 If a sequence context was found, it will be appended in a new column to the right of the existing columns. \
70 When another sequence context was found for the same peptide, it will appended as an extra row in the output.
71 Protein accession numbers / IDs must be in the same format as was used in the FASTA file with protein sequences (database). \
72 The only exception to this rule is that accession numbers / IDs may be optionally suffixed with the peptide\'s position in its protein between brackets. \
73 For example: CLH1_HUMAN[1612-1620] will be matched to CLH1_HUMAN in a FASTA file with protein sequences. \
74 Amino acids in the petide sequences must be in uppercase.
75
76 ===============================================
77 *Protein sequences*
78 ===============================================
79
80 Input file containing all protein sequences in FASTA format. \
81 This tool will look for any type of protein ID in the first part of FASTA sequence headers up until the first white space. \
82 Optionally multiple IDs may be present separated with pipe symbols (|) or semicolons (;). \
83 Optionally IDs may be prefixed with a database namespace and a colon (:). \
84 For example the accession number P32234 as well as the ID 128UP_DROME would be recognized in both this sequence header:
85
86 >UniProtAcc:P32234|UniProtID:128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
87
88 and in this one:
89
90 >P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
91
92 ===================================================
93 *N-terminal and C-terminal sequence context length*
94 ===================================================
95
96 Integers specifying the length of the N-terminal and C-terminal sequence context to retrieve starting from the peptide termini. \
97 So the total sequence context length for a peptide will be:
98 (N-terminal sequence context) + (length of the peptide) + (C-terminal sequence context).
99
100 ===============================================
101 *Padding character*
102 ===============================================
103
104 Optional padding character to fill N-terminal or C-terminal positions in the sequence context, \
105 when the protein was too short to get a complete sequence context. \
106 Defaults to - a.k.a. dash or alignment gap character. \
107
108 -----
109
110 **Getting input data**
111
112 .. _my folder utility: http://mascotinternal.chem.uu.nl/mascot/cgi/uu_myfolder.pl
113
114 This tool requires \
115 peptide sequences in TAB delimited format and \
116 protein sequences from which the peptides were derived in FASTA format. \
117 If your peptide sequences are not in TAB delimited format, you can convert from:
118
119 - FASTA format using *FASTA manipulation* -&gt; *FASTA-to-Tabular*
120 - A format using a different delimiter using *Text Manipulation* -&gt; *Convert*
121
122 When your peptides were derived from a mass spectrometry experiment and identified with a search engine like Mascot, Sequest, etc.,\
123 please make sure you provide the same FASTA database for this tool as the one used for your search.
124 If you used Mascot hosted by the Biomolecular Mass Spectrometry and Proteomics Group @ Utrecht University, \
125 you can use the `my folder utility`_ to download the FASTA databases from the Mascot server.
126
127 -----
128
129 **Examples**
130
131 Example input for peptides identified with a Mascot search, \
132 some with phosphorylated residues indicated by pS, pT or pY \
133 and in TAB delimited format::
134
135 sequence score peptide mr mass delta (abs) mass delta (ppm) all protein matches
136 AGNAARDN 54.24 787.357254 -4.223E-5 -0.05334300253990 H2A1B_HUMAN[67-74]
137 KLpSAAVVLI 11.48 912.600784 0.001608 1.7619971713721432 OSGI2_HUMAN[405-413]
138 RAGIKVpTVA 23.01 913.570892 6.283E-5 0.06786555979719196 PARK7_HUMAN[28-36]
139 KGGVVGIKVD 44.61 970.581146 -0.001214 -1.2507970147608864 P04075[101-110]
140 KIKELQAF 11.87 975.575287 0.003907 4.00481649347068 O60882[71-78]
141 KIpSGpTVNIR 57.17 986.587265 -0.002761 -2.798536022051734 SYTC_HUMAN[681-689]
142 KLpYEALKF 17.54 1010.580032 0.004782 4.731935966057164 F105A_HUMAN[238-245]
143 KLDApSEpSLR 31.31 1017.545441 -0.002377 -2.3360136110127785 CLH1_HUMAN[1612-1620]
144
145 ===============================================
146 *Appending peptide sequence contexts*
147 ===============================================
148
149 With these options:
150
151 - c6 as *Protein identifier column*
152 - c1 as *Peptide sequence column*
153 - 5 as *N-terminal sequence context length*
154 - 5 as *C-terminal sequence context length*
155 - a suitable FASTA database with *Protein sequences*
156 - and everything else set to defaults
157
158 the example above will generate a result like this::
159
160 AGNAARDN 54.24 787.357254 -4.223E-5 -0.05334300253990 H2A1B_HUMAN[67-74] EILELAGNAARDNKKTRI
161 KLpSAAVVLI 11.48 912.600784 0.001608 1.7619971713721432 OSGI2_HUMAN[405-413] LKKIFKLSAAVVLIGSHPN
162 RAGIKVpTVA 23.01 913.570892 6.283E-5 0.06786555979719196 PARK7_HUMAN[28-36] VDVMRRAGIKVTVAGLAGK
163 KGGVVGIKVD 44.61 970.581146 -0.001214 -1.2507970147608864 P04075[101-110] QVIKSKGGVVGIKVDKGVVP
164 KIKELQAF 11.87 975.575287 0.003907 4.00481649347068 O60882[71-78] NSMIRKIKELQAFFGLQV
165 KIpSGpTVNIR 57.17 986.587265 -0.002761 -2.798536022051734 SYTC_HUMAN[681-689] VGEKEKISGTVNIRTRDNK
166 KLpYEALKF 17.54 1010.580032 0.004782 4.731935966057164 F105A_HUMAN[238-245] AILEYKLYEALKFIMLYQ
167 KLDApSEpSLR 31.31 1017.545441 -0.002377 -2.3360136110127785 CLH1_HUMAN[1612-1620] LTKVDKLDASESLRKEEEQ
168
169 Note the header line was ignored.
170
171 </help>
172 </tool>