11
|
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>
|