[phenixbb] Two ions at same position
rdo20 at cam.ac.uk
Fri Aug 8 07:12:34 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?
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
Cambridge CB2 0XY
tel: +44(0)1223 763234
mobile: +44(0)7712 887162
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