diff tools/protein_analysis/tmhmm2.xml @ 11:99b82a2b1272 draft

Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz)

--- 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.