help with installation of psipred
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5.9 years ago
pingEde ▴ 40

Hello! Does anyone install psipred ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README) ? In the file README is reported that after you install psipred: "You must also install the PSI-BLAST and Impala software from the NCBI toolkit, and also install appropriate sequence data banks. The NCBI toolkit can be obtained from URL ftp://ftp.ncbi.nih.gov PSI-BLAST executables can be obtained from ftp://ftp.ncbi.nih.gov/blast"

I don't understand what I have to take from NCBI toolkit and how I can install it. I am sorry if maybe the question is stupid :) Thank you in advance for your help

psipred install ncbi toolkit psi-blast • 2.7k views
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5.9 years ago
arronslacey ▴ 280

what operating system are you using?

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I use Linux (CentOS)

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5.7 years ago

I maintain the PSIPRED code. If you're following the regular instructions just download the regular blast release (not BLAST+) and install it. ftp://ftp.ncbi.nih.gov/blast/executables/legacy/ Follow it's instructions to get blast working.

For PSIPRED we advise you use the uniref90 sequence database and run blast's formatdb command over it to generate the appropriate blast database files.

Once those are done you can edit the runpsipred script to tell psipred where you blast and uniref90 databases are.

If you'd rather use the newer BLAST+ you can use the scripts in PSIPRED's blast+/ directory. Just download blast+, install and then configure the psipred blast+ script as before. Note that BLAST+ support is somewhat experimental atm.

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