[phenixbb] local BLAST server

R.D. Oeffner rdo20 at cam.ac.uk
Fri Aug 8 07:14:14 PDT 2014


Hi,

I'm in the process of installing a local BLAST server for doing blast
protein queries. As I understand it I need a file with all the FASTA
sequences as input for initially generating my local BLAST database.
The one present in
ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt seems to
contain redundant entries. Querying it produces many extra PDB
chain-ids when compared to a BLAST query on the NCBI web server.

Does anyone know where to get a non-redundant version of FASTA records
so that I can create a similar database as the one used by NCBI?


Many thanks,

Rob

-- 
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234
mobile: +44(0)7712 887162


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