Databases supported at BMERC



Table of Contents


I. PDB

We support here at BMERC:

Locally supported PDB formats:

  1. PDB_BLAST_Format: /structure/pdb.blast/pdb.blast
  2. PDB_TABLE_Format: /structure/pdb.tbl/pdb.tbl
  3. PDB_IG_Format: /structure/pdb.tbl/pdb.ig
  4. PDB_Key_Format: /structure/pdb.key/pdb.keyword
  5. PDB_EC_numbers: /structure/pdb.key/pdb.EC-numbers
  6. PDB_DSSP_Format: /structure/dssp
  7. PDB_Smoothed_dssp: /structure/smoothed_dssp
The PDB databases are updated on the weekly basis.

II. Genomes

BMERC Completed Genomes collected resources


III. Translated-GenBank

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:

  1. TRANSLATED_GENBANK_Short_Dir: /seq/gb-176.pep/all.sdir
  2. TRANSLATED_GENBANK_BLAST_Format: /seq/gb-176.pep.blast/
  3. TRANSLATED_GENBANK_TABLE_Format: /seq/gb-176.pep.tbl/
  4. TRANSLATED_GENBANK_DEFS_Format: /seq/gb-176.pep.aux/all.defs


IV. NBRF-PIR


                        * 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:
  1. Protein_Database: /seq/nbrf-80.dat/protein.dat
  2. Protein_Database_New: /seq/nbrf-80.dat/new.dat
  3. Protein_Database_Blast_Format: /seq/nbrf-80.blast/nbrf-80
  4. Protein_Database_Table_Format: /seq/nbrf-80.tbl/nbrf-80.tbl
  5. Protein_Database_IG_Format: /seq/nbrf-80.pep/nbrf-80.pep

V. SWISSPROT-TREMBL

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:
  1. Swissprot_ig: /seq/swissprot-57.pep/all.pep
  2. AllLoci: /seq/swissprot-57.aux/all.defs
  3. Accession_Numbers: /seq/swissprot-57.aux/swissprot-57.acc-numbers
  4. EC_Numbers: /seq/swissprot-57.aux/swissprot-57.ec-numbers
  5. Keywords: /seq/swissprot-57.aux/swissprot-57.keywords
  6. Taxonomy: /seq/swissprot-57.aux/swissprot-57.taxonomy
  7. Tables: /seq/swissprot-57.tbl/all.tbl
  8. Titles: /seq/swissprot-57.tbl/all.titles
  9. Lengths: /seq/swissprot-57.tbl/all.len
  10. Blast_Format: /seq/swissprot-57.blast/swissprot-57
  11. Blast_Format_Trembl: /seq/trembl.blast/trembl

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.


VI. UniRef

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:
  1. UniRef100_Tables: /seq/uniref/uniref100.tbl
  2. UniRef100_Blast_Format: /seq/uniref/uniref100
  3. UniRef90_Tables: /seq/uniref/uniref90.tbl
  4. UniRef90_Blast_Format: /seq/uniref/uniref90
  5. UniRef50_Tables: /seq/uniref/uniref50.tbl
  6. UniRef50_Blast_Format: /seq/uniref/uniref50

VII. PIR-NREF

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:
  1. PIR-NREF_Tables: /seq/pir-nref/pir-nref.tbl
  2. PIR-NREF_Blast_Format: /seq/pir-nref/pir-nref

VIII. NR

        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":

  1. PIR-NREF_Blast_Format: /seq/NR/nr.00
  2. PIR-NREF_Blast_Format: /seq/NR/nr.01
  3. PIR-NREF_Blast_Format: /seq/NR/nr.02

IX. Pfam

Pfam is a collection of protein families and domains.

Locally supported Pfam formats:
  1. Pfam_BLAST_Format: /seq/pfam/pfam.fa
  2. Pfam_Table_Format: /seq/pfam/pfam.tbl
  3. Pfam_Defs_Format: /seq/pfam/pfam.defs

X. Pima_Profile

pima_profile - prior based profile construction program - local program written at BMERC

PIMA profile search at BMERC

The local PROFILE_HOME=/seq/pima_profile


Esther Epstein