Hi, I have psipred working (thanks to some posters on here) and can confirm it works for single sequences - however when I input a fasta file with multiple sequences it only gives the output for the last sequence in the file. does anyone know how to get round this?
here is the runpsipred.pl script:
#!/bin/tcsh
# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED V3 prediction using BLAST+. Note that it
# assumes that the following programs are in the appropriate directories:
# psiblast - PSIBLAST executable (from NCBI BLAST+)
# psipred - PSIPRED V3 program
# psipass2 - PSIPRED V3 program
# chkparse - PSIPRED V3 program
# NOTE: Experimental PSIPRED script with BLAST+ compatability (DTJ May 2010)
# The name of the BLAST+ data bank
set dbname = uniref90filt
# Where the NCBI BLAST+ programs have been installed
set ncbidir = /usr/local/bin
# Where the PSIPRED V3 programs have been installed
set execdir = ../bin
# Where the PSIPRED V3 data files have been installed
set datadir = ../data
set basename = $1:r
set rootname = $basename:t
# Generate a "unique" temporary filename root
set hostid = `hostid`
set tmproot = psitmp$$$hostid
\cp -f $1 $tmproot.fasta
echo "Running PSI-BLAST with sequence" $1 "..."
$ncbidir/psiblast -db $dbname -query $tmproot.fasta -inclusion_ethresh 0.001 -out_pssm $tmproot.chk -num_iterations 3 -num_alignments 0 >& $tmproot.blast
if ($status != 0) then
tail $tmproot.blast
echo "F ...