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comparison splicesite_maxent.xml @ 11:7ffb2ec6f557

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author xuebing
date Sun, 01 Apr 2012 08:23:53 -0400
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1 <tool id="maxent" 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="maxent_score5.pl" selected="true">5' splice site</option>
8 <option value="maxent_score3.pl">3' splice site</option>
9 </param>
10
11 </inputs>
12 <outputs>
13 <data format="tabular" name="out_file1" />
14 </outputs>
15 <help>
16
17 **What it does**
18
19 This tool computes splice site scores using a max entropy model. See more details here:
20
21 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
22
23 -----
24
25 **Example input for 5' splice site sequence**
26
27 3 exonic and 6 intronic nucleotides flanking the junction::
28
29 CTGGTGAGT
30 AAGGTACAG
31
32 or fasta format::
33
34 >seq1
35 CTGGTGAGT
36 >seq2
37 AAGGTACAG
38
39 Output::
40
41 CTGGTGAGT 10.10
42 AAGGTACAG 8.04
43
44 or fasta format::
45
46 >seq1 CTGGTGAGT 10.10
47 >seq2 AAGGTACAG 8.04
48
49
50 -----
51
52 **Example input for 3' splice site sequence**
53
54 3 exonic and 20 intronic nucleotides flanking the junction::
55
56 CCTGCATCCTCTGTTCCCAGGTG
57 TTTCTTCCCTCCGGGAACAGTGG
58
59 Output::
60
61 CCTGCATCCTCTGTTCCCAGGTG 10.47
62 TTTCTTCCCTCCGGGAACAGTGG 6.22
63
64 </help>
65 </tool>