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comparison tools/mytools/splicesite.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="splicesite" name="splice site score">
2 <description>using max entropy model</description>
3 <command interpreter="perl">$script $input > $out_file1 </command>
4 <inputs>
5 <param name="input" format="txt" type="data" label="Sequence file" help="fasta or raw sequence (one sequence per line)"/>
6 <param name="script" type="select" label="Select model">
7 <option value="splicesitescore/score5.pl" selected="true">5' splice site</option>
8 <option value="splicesitescore/score3.pl">3' splice site</option>
9 </param>
10 </inputs>
11 <outputs>
12 <data format="tabular" name="out_file1" />
13 </outputs>
14 <help>
15
16 **What it does**
17
18 This tool computes splice site scores using a max entropy model. See more details here:
19
20 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
21
22 -----
23
24 **Example input for 5' splice site sequence**
25
26 3 exonic and 6 intronic nucleotides flanking the junction::
27
28 CTGGTGAGT
29 AAGGTACAG
30
31 or fasta format::
32
33 >seq1
34 CTGGTGAGT
35 >seq2
36 AAGGTACAG
37
38 Output::
39
40 CTGGTGAGT 10.10
41 AAGGTACAG 8.04
42
43 or fasta format::
44
45 >seq1 CTGGTGAGT 10.10
46 >seq2 AAGGTACAG 8.04
47
48
49 -----
50
51 **Example input for 3' splice site sequence**
52
53 3 exonic and 20 intronic nucleotides flanking the junction::
54
55 CCTGCATCCTCTGTTCCCAGGTG
56 TTTCTTCCCTCCGGGAACAGTGG
57
58 Output::
59
60 CCTGCATCCTCTGTTCCCAGGTG 10.47
61 TTTCTTCCCTCCGGGAACAGTGG 6.22
62
63 </help>
64 </tool>