MMTSB
Tool Set Documentation

Difference between revisions of "Psipred.pl"

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== Description ==
 
== Description ==
  
 +
This script calls PSIPRED to carry out secondary structure prediction for the given sequence. The sequence is read from a file which should contain only the one-letter amino acid sequence either on a single or on multiple lines.<BR>
 +
 +
In order for this script to work, PSIPRED and BLAST/PSI-BLAST along with the
 +
recent sequence databases (nr, swissprot, pdbaa) should be installed.
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The location of the PSIPRED installation can be provided through the environment variable <TT>PSIPREDDIR</TT>.<BR>
  
 
== Options ==
 
== Options ==
  
 
; -help : usage information
 
; -help : usage information
 
+
; -long : long output format
  
 
== Examples ==
 
== Examples ==
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<mmtsbToolExample cmd="psipred.pl" set="test1"></mmtsbToolExample>
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<mmtsbToolExample cmd="psipred.pl" set="test2"></mmtsbToolExample>

Latest revision as of 22:54, 13 September 2010

Usage

usage:   psipred.pl [options] [seqFile]
options:            [-long]
Show source


Description

This script calls PSIPRED to carry out secondary structure prediction for the given sequence. The sequence is read from a file which should contain only the one-letter amino acid sequence either on a single or on multiple lines.

In order for this script to work, PSIPRED and BLAST/PSI-BLAST along with the recent sequence databases (nr, swissprot, pdbaa) should be installed. The location of the PSIPRED installation can be provided through the environment variable PSIPREDDIR.

Options

-help 
usage information
-long 
long output format

Examples

psipred.pl sequence
predicts the secondary structure for the given sequence

CCEEEEEEEECCEECCEEEEEECCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCEECCCCEECCCCCCCEEECCCCCCCCCEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCCCCEEEEEEEECCHHHHHHHHCCCCCCCCCEECCEEEEECCEECC


psipred.pl -long sequence
predicts the secondary structure for the given sequence and writes out the results in long format

   1 R C   0.996  0.002  0.001
   2 P C   0.886  0.005  0.093
   3 R E   0.193  0.000  0.799
   4 C E   0.065  0.000  0.914
   5 F E   0.061  0.000  0.937
   6 F E   0.038  0.000  0.937
   7 D E   0.068  0.000  0.941
   8 I E   0.087  0.001  0.933
   9 A E   0.116  0.002  0.859
  10 I E   0.130  0.002  0.828

...