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I am trying to install psipred in a unix server.

Psipred is installed, but fails because it can not find the correct database files. I have downloaded uniprod90.fasta. Psipred also loads the old legacy ncbi BLAST-2.2.26 and BLAST+.
runpsipred and runpsipredplus have been patched to call the correct version of BLAST.

I have run a few commands to index the uniprod90 database: 

pfilt uniref90.fasta > uniref90filt
formatdb -t uniref90filt -i uniref90filt
makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta

I then ran psipred and got this error:

$ ./psipred/example/example.fasta
Running PSI-BLAST with sequence  ./psipred/example/example.fasta ...
[blastpgp] WARNING: Unable to open uniref90.pin
[blastpgp] WARNING: Unable to open uniref90.pin
FATAL: Error whilst running blastpgp - script terminated!

makeblastdb created 26 pin files, but not uniref90.pin.

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Try with:

makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90

The -out is the name of the DB. So if you use uniref90.fasta, it creates uniref90.fasta.pinwhile the script seems to be expectinguniref90.pin`.

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