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Difference between revisions of "psipred.pl"
From MMTSB
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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. | ||
| + | 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 == | ||
| + | <mmtsbToolExample cmd="psipred.pl" set="test1"></mmtsbToolExample> | ||
| − | + | <mmtsbToolExample cmd="psipred.pl" set="test2"></mmtsbToolExample> | |
| − | <mmtsbToolExample cmd=" | ||
Latest revision as of 15:19, 30 July 2009
Usage
usage: psipred.pl [options] [seqFile] options: [-long]
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 ...