[phenixbb] local BLAST server

[R.D. Oeffner]

Thanks very much!

Rob

On 2014-08-08 16:19, Zhijie Li wrote:
> Hi Rob,
> 
> Update:
> 
> You may want to check the pdbaa.gz first. It seems this is the PDB
> subset of the nr database.
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/pdbaa.gz
> 
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/README says:
> pdbaa.*tar.gz          | protein sequences from pdb protein
> structures, | its parent database is nr.
> 
> Zhijie
> 
> ===============
> Hi Rob,
> 
> The BLAST nr database (fasta format) can be downloaded from the NCBI 
> ftp:
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
> As I remember it is the nr.gz file. When unzipped the file is called 
> "nr".
> 
> According to BLAST the nr database does contain PDB entries.
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide
> 
> It is significantly larger than the PDB data file you are currently 
> using.
> You might consider extract all the PDB sequences from it so that you do 
> not
> need to go through all the non-PDB sequences.
> 
> Zhijie
> 
> -----Original Message----- From: R.D. Oeffner
> Sent: Friday, August 08, 2014 10:14 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] local BLAST server
> 
> 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
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