We support here at BMERC:
Locally supported PDB formats:
NCBI-GenBank Flat File Release 176.0 FTP Site: ftp.ncbi.nih.gov Directory: ncbi-asn1/protein_fasta URL: ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/ Release Date: February 15, 2010
The supported Translated Genbank formats:
* PIR-PSD Final Release * ========================= Release 80.00 is the final release for the PIR-International Protein Sequence Database (PIR-PSD). In 2002, PIR joined EBI and SIB to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. This final version of the database will be accessible from the PIR web site and downloadable from the FTP site.The supported NBRF-PIR formats:
Swiss-Prot and TrEMBL databases are part of UniProt Knowledgebase database, which is the central access point for extensive curated protein information, including function, classification, and cross-reference. The Swiss-Prot Protein Knowledgebase (fully annotated curated entries) and the TrEMBL Protein Sequence Database (computer-generated entries enriched with automated classification and annotation) are updated on the biweekly basis.The supported Swissprot & Trembl formats:
Detailed release statistics for TrEMBL and Swiss-Prot sections of the UniProt Knowledgebase can be viewed at http://www.ebi.ac.uk/swissprot/sptr_stats/index.html and http://www.expasy.org/sprot/relnotes/relstat.html respectively.
The UniProt Reference Clusters (UniRef) is one of three components of UniProt (Universal Protein Resource) combines closely related sequences into a single record to speed searches.
The /seq/uniref directory contains the biweekly updates of the UniProt Reference Clusters (UniRef). There are three UniRef databases based on different sequence identity cut-offs: uniref100(100%), uniref90(90%) and uniref50(50%).The supported UniRef formats:
PIR-NREF a comprehensive database for sequence searching and protein identification, contains non-redundant protein sequences from PIR-PSD, Swiss-Prot, TrEMBL, RefSeq, GenPept, and PDB.The supported PIR-NREF formats:
FTP Site: ftp.ncbi.nih.gov Directory: blast/db/ URL:ftp://ftp.ncbi.nih.gov/blast/db The NR Database is the replacement for PIR-NREF database. There are three blastable NR databases: "nr.00", "nr.01", "nr.02":
Pfam is a collection of protein families and domains.Locally supported Pfam formats:
pima_profile - prior based profile construction program - local program written at BMERCPIMA profile search at BMERC
The local PROFILE_HOME=/seq/pima_profile