Question: help with installation of psipred
0
gravatar for pingEde
3.6 years ago by
pingEde30
European Union
pingEde30 wrote:

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

ADD COMMENTlink modified 3.4 years ago by daniel.buchan0 • written 3.6 years ago by pingEde30
0
gravatar for arronslacey
3.6 years ago by
arronslacey260
United Kingdom
arronslacey260 wrote:

what operating system are you using?

ADD COMMENTlink written 3.6 years ago by arronslacey260

I use Linux (CentOS)

ADD REPLYlink written 3.6 years ago by pingEde30
0
gravatar for daniel.buchan
3.4 years ago by
daniel.buchan0 wrote:

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.

ADD COMMENTlink written 3.4 years ago by daniel.buchan0
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