Databanks available at the Belgian EMBNet Node (BEN)

Check out the databanks at BEN
Search the databanks using the Sequence Retieval System (SRS)

• EMBL / EMBLNEW
  The European Molecular Biology Laboratory databank is meant to contain all DNA and RNA sequences that have ever been published, including sequences from patents. It is maintained at the European Bioinformatics Institute, an outstation of the EMBL at Hinxton (England). The last major release (51) contains 1438050 sequences with a total of more than 931.10, bases. The table EMBL contains the last release, the table EMBLNEW contains sequences that were added since the last release and that BEN retrieves each night from the EBI site.
• GENBANK / GENBANKNEW
  GenBank is maintained at the National Center for Biotechnology Information (NCBI, Bethesda, Maryland). NCBI is the American counterpart of EMBL. An agreement exists between EMBL, GenBank and the DNA Data Bank of Japan managers to exchange submitted sequences and to attribute them the same accession number. At the BEN site we need to keep only the small set of GenBank sequences (a few thousands) that are not present in EMBL.
  From EMBL/EMBLNEW and GENBANK/GENBANKNEW, we build everyday our non-redundant nucleic acids databank for the GCG software.
• SWISSPROT / SWISSNEW
  SWISS-PROT is maintained at the University of Geneva under the direction of Amos Bairoch, in collaboration with the EBI. It is a general protein sequence databank, containing translations of open reading frames identified in DNA as well as results from genuine protein sequencing. The sequences are accompanied by a carefully edited and very valuable documentation, including many cross-references to other databanks. BEN retrieves each week new sequences from the Expasy site at Geneva
• PIR
  The Protein Information Resource is another general protein databank, maintained at the National Biomedical Research Foundation (Georgetown, Washington), in collaboration with the Munich Information Center for Protein Sequences (MIPS, Germany). At the BEN site we keep only the set of PIR sequences that are not found in SWISS-PROT (the exclusion is based on cross-references in the databank). We have however arranged that entries retrieved from SWISSPROT/SWISSNEW at the BEN site contain a hyperlink pointing to the corresponding PIR entry at the SRS server of the EBI, so that the interested user can access it easily.
• GENPEPT / GENPEPTNEW - translations of open reading frames identified in GenBank sequences. At the BEN site a set non-redundant with SWISS-PROT and PIR is updated weekly.
  From SWISSPROTISWISSNEW, PIR and GENPEPTIGENPEPTNEW, we build every week our non-redundant Protein databank for the GCG software.
• VECTOR -
  vector-ig is a databank of vector sequences including plasmids, phagemids, phasmids, cosmids, phages, and YAC'S.
• AIDSN
  Aidsbase contains sequences from HIV and SIV and a number of related sequences. It is maintained at Los Alamos National Laboratory (New Mexico).
• PDB/PDBNEW
  The Protein Data Bank contains 3D-structures (atomic co-ordinates) of proteins, nucleic acids and complex carbohydrates, as determined by Xray crystallography or NMR. It is maintained at Brookhaven National Laboratory (New York). At the BEN site, the PDB is updated weekly. Under GCG, two databanks of sequences (one with proteins and one with nucleic acids) extracted from the PDB are maintained. The user can perform a fasta similarity search and then retrieve the structures of sequences related to the query sequence by SRS.
• NRL3D
  a databank with protein sequences extracted from PDB entries, created at NBRF.
• HSSP
  Homology-derived Secondary Structure of Proteins contains multiple sequence alignments of proteins from the PDB with related proteins from the SWISSPROT. It is maintained by C. Sander and R. Schneider at the EMBL/EBI.
• PROSITE / PROSITEDOC -
  a databank with the conserved domains of protein families. Most domains are represented as patterns, some as profiles and still others as sets of rules. Each PROSITE entry contains cross-references to matching SWISS-PROT sequences, including the false-positives and false-negatives. It is maintained by A. Bairoch. The patterns from PROSITE are also accessible under GCG (program motif).
• BLOCKS
  Blocks contains gapless multiple sequence alignments corresponding to the PROSITE entries. It is maintained by S. Henikoff & J.Henikoff at the Fred Hutchinson Cancer Research Center (Seattle, Washington).
• PRODOM
  ProDom contains multiple sequence alignments of related proteins from SWISS-PROT. It is maintained by E. Sonnhammer at the Sanger Institute (Hinxton, England) and D. Kahn at the Institut National de la Recherche Agronomique (Toulouse, France).
• ENZYME
  EC contains a list of the enzymes to which an Enzyme Commission number has been attributed. It is maintained by A. Bairoch. With SRS, it is possible to search enzymes by reagent, reaction product or cofactor.
• REBASE - contains restriction enzymes. It is maintained by Dr. R.J. Roberts at New England BioLabs. With SRS, it is possible to search restriction enzymes specific for a particular site. The REBASE is also accessible under GCG, where it is used to map DNA. (Information about the commercial suppliers of the restriction enzymes is available on-line with the GCG command :
• TFSITE / TFFACTOR - TRANSFAC is a databank of eukaryotic transcription factors. It is maintained by the Gesellschaft für Biotechnologische Forschung (Braunschweig, Germany). At the BEN site only part of the databank is installed, the table TFSITE contains information about the binding sites, including references to EMBL sequences that contain them, the table TFFACTOR contains information about the factors themselves, including references to SWISS-PROT and PIR entries with the sequence. BEN has also installed a pattern file transfac.dat to be used with GCG programs as map.
• EPD - The Eukaryotic Promoter Database contains references to EMBL sequences where RNA polymerase 11 transcription start sites have been identified. It is maintained by Philipp Bucher at the Institut Suisse de Recherches Experimentales sur le Cancer (Lausanne, Switzerland). At the BEN site there is also under GCG a sequence databank with the 600 bases around the start site.
• CPGISLE - CpGlsle contains information about CpG islands, including references to EMBL sequences where they have been identified. It is maintained at the Norwegian EMBnet Node.
• ECDC - The E. coli database collection is a databank with information about the Escherichia coli K12 genome. It is maintained at the Justus-Liebig University (Giessen, Germany). At the BEN site, only the table with the individual genes has been installed. With SRS, it is possible to search the genes that have been located at a certain position on the E. coli genetic map.
• SEQANALREF / SEQANALRABS
  SEQANALREF is a databank of literature abstracts in the domain of sequence analysis. It is maintained by A. Bairoch.
  

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