[phenixbb] local BLAST server

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


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,


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

tel: +44(0)1223 763234
mobile: +44(0)7712 887162

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