Re: RPSblast for CDD databases

[Anurag Priyam]

Hi Stephan,

Thanks for the compliment! SequenceServer only supports blastn, blastp, blastx, tblastx, and tblastn algorithms at the moment. This is why you don’t see an option to change blastp to rpsblast. I am sorry that this is not clearly indicated on the website - we will address that.

Priyam

On 25 Apr 2018, at 08:37, 'Stephan Kolkenbrock' via sequenceserver <sequenc...@googlegroups.com> wrote:

Hello!

I recently installed and tested sequenceserver (beta 4). Thank you very much for such a nice and comfortable surface for blasting. This faciliates local blast searches really easy and displays the results quite nicely.
But now to my question: Is it also possible to do a position-specific blast via rpsblast on Cdd-Databases? I just downloaded the Cdd database (ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/Cdd_NCBI_LE.tar.gz),
extracted it and put it in the database directory for sequenceserver. Upon restarting sequenceserver it recognizes it as a aa database, but wants to do a blastp instead of rpsblast. This blast search of course does not work.
Would it be possible to somehow change it to rpsblast, since it is already part of Blast+ 2.6.0 which was downloaded by sequenceserver?

Best wishes,

Stephan

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