Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/tmhmm2.xml @ 11:99b82a2b1272 draft
Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)
author | peterjc |
---|---|
date | Wed, 03 Apr 2013 10:49:10 -0400 |
parents | e52220a9ddad |
children | dc958c2a963a |
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--- a/tools/protein_analysis/tmhmm2.xml Wed Mar 27 11:21:05 2013 -0400 +++ b/tools/protein_analysis/tmhmm2.xml Wed Apr 03 10:49:10 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.9"> +<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.10"> <description>Find transmembrane domains in protein sequences</description> <!-- If job splitting is enabled, break up the query file into parts --> <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> @@ -47,12 +47,19 @@ The input is a FASTA file of protein sequences, and the output is tabular with six columns (one row per protein): - 1. Sequence identifier - 2. Sequence length - 3. Expected number of amino acids in TM helices (ExpAA). If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide). - 4. Expected number of amino acids in TM helices in the first 60 amino acids of the protein (Exp60). If this number more than a few, be aware that a predicted transmembrane helix in the N-term could be a signal peptide. - 5. Number of transmembrane helices predicted by N-best. - 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside) +====== ===================================================================================== +Column Description +------ ------------------------------------------------------------------------------------- + 1 Sequence identifier + 2 Sequence length + 3 Expected number of amino acids in TM helices (ExpAA). If this number is larger than + 18 it is very likely to be a transmembrane protein (OR have a signal peptide). + 4 Expected number of amino acids in TM helices in the first 60 amino acids of the + protein (Exp60). If this number more than a few, be aware that a predicted + transmembrane helix in the N-term could be a signal peptide. + 5 Number of transmembrane helices predicted by N-best. + 6 Topology predicted by N-best (encoded as a strip using o for output and i for inside) +====== ===================================================================================== Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides. @@ -60,6 +67,7 @@ Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. + **Notes** The short format output from TMHMM v2.0 looks like this (six columns tab separated, shown here as a table): @@ -81,6 +89,7 @@ gi|3298468|dbj|BAA31520.1| 107 59.37 31.17 3 o23-45i52-74o89-106i =================================== === ===== ======= ======= ==================== + **References** Krogh, Larsson, von Heijne, and Sonnhammer.