ANNOUNCING PIR-NREF Non-Redundant Reference Protein Database

Pirmail pirmail at NBRF.Georgetown.Edu
Mon Oct 29 20:25:36 EST 2001


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ANNOUNCING PIR-NREF
Containing 800,917 non-redundant protein sequences

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The Protein Information Resource (PIR) is pleased to announce the
beta-release of the
PIR-NREF (Non-redundant REFerence) Protein Database at:

http://pir.georgetown.edu/pirwww/search/pirnref.shtml

The PIR-NREF is designed to provide a timely and comprehensive
collection of all protein
sequence data, keeping pace with the genome sequencing projects and
containing source
attribution and minimal redundancy. The database contains all sequences
in PIR-PSD,
Swiss-Prot, TrEMBL, RefSeq, GenPept, and PDB, and is updated biweekly.
Non-redundancy is
achieved based on clustering by sequence identity and taxonomy at the
species level.  The
NREF report provides source attribution with protein IDs and names from
associated
databases, in addition to protein sequence, taxonomy, and bibliography.

The web site supports direct retrieval of NREF reports based on sequence
unique
identifiers, as well as full-scale BLAST search and peptide/pattern
match for functional
identification of query proteins or peptides. The results are linked to
the underlying
databases for retrieval of up-to-date source entries.

An example NREF entry is at:
http://pir.georgetown.edu/iproclass/nfretr.html

An example BLAST search output is at:
http://pir.georgetown.edu/iproclass/NFBLASTex.html

The database is downloadable in XML format (data file) and FASTA format
(sequence file)
from our FTP site at:
ftp://nbrfa.georgetown.edu/pir_databases/nref/

Please visit the pages and give us your feedback!

The work is supported in part by NIH Grant# P41 LM05798.

Please contact Cathy Wu at wuc at nbrf.georgetown.edu for any comments and
suggestions, and
for inquiries regarding setting up reciprocal links or mirror site

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