nrdb program

[poisson200]

Hi there,
Does anyone know a link to download the nrdb program that removes redundancy from a file of sequences? I looked around the NCBI but did not actually find it.

If anyone has a copy or knows a link to one, it will be most appreciated.

Thank you

[Torst]

Does anyone know a link to download the nrdb program that removes redundancy from a file of sequences? I looked around the NCBI but did not actually find it.

It comes with the WU-BLAST distribution: http://blast.wustl.edu/

The EBI Exonerate software comes with "fastanrdb" equivalent: http://www.ebi.ac.uk/~guy/exonerate/

BioPerl comes with a "bp_nrdb.pl" equivalent: http://bioperl.org/

[poisson200]

Great, thank you

Dear Torst.
That is great. I knew about Wublast but if you check their website, it has been handed over to a company that now charge all to use it.

But fastanrdb sounds great.

Thank you.

John.

[Torst]

That is great. I knew about Wublast but if you check their website, it has been handed over to a company that now charge all to use it.

Yes I know, but you can get a personal licence for free: http://blast.advbiocomp.com/licensing/

As you only want "nrdb" (assuming it is still part of the package) you won't be violating any "publish results of" clauses?

[hpm]

nrdb freely available from AB-BLAST web site

While nrdb 3.0 was bundled with the last version of WU-BLAST (and presumably is with AB-BLAST). nrdb 2 was also freely available (i.e. not requiring a WU-BLAST license) as a separate download from the web site. Checking on the AB-BLAST web site this is still the case, so you can download pre-built executables or the source for nrdb from:

http://blast.advbiocomp.com/pub/nrdb/