-This is a program which predicts the secondary structure of a sequence given a path to a FASTA sequence.
-It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
+This is a program which predicts the secondary structure of a protein sequence given a path to a
+FASTA sequence. It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
The program is primarily design for use by the Jpred server, but it can be used directly by any user.
Some of the output may not be meaningful if used directly - it can be safely ignored.
The program is primarily design for use by the Jpred server, but it can be used directly by any user.
Some of the output may not be meaningful if used directly - it can be safely ignored.
@@ -20,41+20,50 @@ Some of the output may not be meaningful if used directly - it can be safely ign
=over 5
=over 5
-=item -sequence path to input FASTA file
+=item -in/-sequence FILE
-The path to the sequence (in FASTA format) you want to predict.
+The path to the sequence file (in FASTA format) you want to predict.
-=item -output file
+=item -out/-output FILEPREFIX
-A prefix to the filenames created by Jpred, defaults to the value set by --sequence.
+A prefix to the filenames created by Jpred, defaults to the value set by -sequence/-in.
-=item --db database
+=item -dbpath PATH
-Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code. Crap I know, but that's the way it is at the moment. It's probably best to stick the default for the time being.
+Path to the uniref database used for PSI-BLAST querying.
+Default: .
+=item -dbname database
+
+Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code.
Default: uniref90
=item -psi path
Path to a PSIBLAST output file.
Default: uniref90
=item -psi path
Path to a PSIBLAST output file.
-=item --pred-nohits
+=item -ncpu NNN
+
+Number of CPU used by jpred.pl. Maximum value is 8
+Default: NNN = 1
+
+=item -pred-nohits
Toggle allowing Jpred to make predictions even when there are no PSI-BLAST hits.
Toggle allowing Jpred to make predictions even when there are no PSI-BLAST hits.
-=item --verbose
+=item -verbose
Verbose mode. Print more information while running jpred.
Verbose mode. Print more information while running jpred.
-=item --debug
+=item -debug
Debug mode. Print debugging information while running jpred.
Debug mode. Print debugging information while running jpred.
-=item --help
+=item -help
Gives help on the programs usage.
Gives help on the programs usage.
-=item --man
+=item -man
Displays this man page.
Displays this man page.
@@ -66,7+75,7 @@ Can't cope with gaps in the query sequence.