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Databases maintained locally by ACHS

A List of locally stored databases and their latest updates. Databases are stored on an Apple XServe RAID mounted on the ACHS bioinformatics server, watson.achs.virginia.edu. These databases are accessed through GCG/SeqWeb.

	Release #	Release or Upgrade date
GenBank (gb_new division updated nightly	Release 166.0	06/15/08
NCBI RefSeq, complete release (DNA & protein - updated nightly)	Release 27.0	01/06/08
GenPept (gp_new division updated nightly)	Release 166.0	06/16/08
PIR_Protein - no longer updated - use UniProt instead	Release 80	01/2005
SWISS-PROT - no longer updated - use Uniprot instead	Release 44	01/2005
UniProt (both uniprot_swissprot and uniprot_trembl - updated weekly) UniProt is a combination of the information previously contained in the separate databases SwissProt, TrEMBL and PIR	Release 11.0 new (07/04)	05/29/07
H. sapiens reference genome (build 36, version 2)	NCBI constructs	09/2006
M. musculus reference genome (build 36, version 1)	NCBI constructs	05/2006
D. rerio reference genome (build 1, version 1)	NCBI constructs	07/2005
C. elegans genome	NCBI constructs	01/2003
Yeast Genome Database	original	05/1998
Yeast - genbank entries (yeast_gb)	N/A	03/2006
Yeast - complete genome (yeast_chr) from NCBI RefSeq constructs	N/A	03/2006
Yeast Genome Peptide database	original	05/1998
Yeast - non-redundant protein entries (yeastpep_nr)	N/A	03/2006
Yeast ORF Database (no introns)	N/A	03/2006
PROSITE	Release 18.26	05/11/04
Transcription Factor Database (no longer updated)	3.4	06/01/99
Pfam	21.0	11/2006
Restriction Enzyme	REBASE 612	11/ 30/2006

notes on referencing databases from within GCG

notes on referencing BLAST databases within GCG

GenBank

A copy of the GenBank DNA database is maintained on site. The database is updated daily.

• GenBank release notes
• Link to the GenBank master copy at NCBI
• The GenBank master copy at NCBI is also accessable through Entrez

RefSeq

RefSeq provides reference sequence standards for genomes, transcripts and proteins. Updated weekly.

• RefSeq release notes
• NCBI's RefSeq web site
• NCBI HandBook- GenBank versus RefSeq

GenPept

A protein database consisting of the translated protein sequences, contained in the GenBank sequence headers. Most sequences are hypothetical and not confirmed experimentally. The database is divided into the same subdivisions as GenBank. Updated daily.

• GenPept release notes

UniProt *NEW*

The Universal Protein Resource is a repository of protein sequence and function. The data in UniProt comes from combining the information contained in Swiss-Prot, TrEMBL, and PIR. It consists of two major sections - uniprot_sw (manually curated and annotated entries from SwissProt and PIR), and uniprot_tr (computer analyzed entries from TrEMBL and PIR, awaiting full manual curation and annotation).

Since UniProt is wholly redudant with PIR, eventually (ie. end of 2004, or early 2005) production/updates of the PIR protein sequence database will cease. UniProt is updated bi-weekly.

• The UniProt organization home page (and the uniprot site at ExPASy)
• Link to the release notes at ExPASy.org

PIR

A protein database. Discontinued in January 2005 - replaced with UniProt. Version 80 will remain available, but users should access UniProt for the most recent, and accurate protein sequences.

• PIR release notes
• Link to the PIR master database at Georgetown.

SWISSPROT

A well annotated protein database.

As of January 2005, SwissProt has been replaced by UniProt. The last update of Swissprot was version 44.2 on January, 2005. This last version will remain available, but users should access UniProt for the most recent, and accurate protein sequences.

H. sapiens

Individual chromosome builds from a reference assembly for the whole genome.

• release notes (UVa maintains a copy of the Public Sequencing Consortium's reference build, not the Celera Genomics' alternative build)
• Link to the chromosome browser page at NCBI (the local database was built from the files available at NCBI's FTP site - see the "genomes" folder at ftp.ncbi.nih.gov)

M. musculus

Individual chromosome builds from a reference assembly for the whole genome (includes mitochondrial genes and unannotated fragments)

• release notes (UVa maintains a copy of the Public Sequencing Consortium's reference build, not the Celera Genomics' alternative build)
• Link to the chromosome browser page at NCBI (the local database was built from the files available at NCBI's FTP site - see the "genomes" folder at ftp.ncbi.nih.gov)

D. rerio

Individual chromosome builds from a reference assembly for the whole genome (includes mitochondrial genes and unannotated fragments)

• release notes
• Link to the chromosome browser page at NCBI (the local database was built from the files available at NCBI's FTP site - see the "genomes" folder at ftp.ncbi.nih.gov)
• Link to the master Zebrafish genome site at the Sanger Institute

Caenorhabditis elegans

• Link to the Sanger Center's nematode database

Yeast Genome Databases

The yeast_orf database has been updated and reinstated. This version of the Sanger orf database contains orf sequences with no introns.

Three new databases have been added locally: yeast_gb, yeastpep_nr, and yeast_chr. These are:

1. The full contingent of GenBank entries taken from the complete yeast genome.
2. The full contingent of non-redundant S. cerevisiae protein entries from SWISSPROT, PIR,, and GenPept.
3. The complete yeast genome (16 chromosomes plus mtDNA), annotated by chromosome number.

Because the format of these new yeast databases differs slightly from our older databases, the original databases are still available:

• The original (and incomplete!) yeast genome nucleotide database can be searched (as before) from GCG through FASTA by specifying: yeast:*
• The original (and out-of-date!) yeast genome peptide database can be searched from GCG through FASTA by specifying: yeastpro:*, or yeastpep:*

• A link to the master Saccharomyces Genome Database. This site contains useful yeast-related topics.

Restriction enzyme database

The file containing all the restriction enzyme sites used in GCG can be downloaded with the GCG command: fetch enzyme.dat. The file is updated monthly.

• The REBASE release notes
• The REBASE site.

Transcription factor database

The file containing all the transcription factor sites used in GCG can be downloaded with the GCG command: fetch tfsites.dat.

TRANSFAC is no longer available freely for updates/downloads. Hence, our local copy is very out of date.

For the most current version of TRANSFAC, please go to the BioBase Corp. web site

other Web-based TRANSFAC search engines

• The TRANSFAC Home Page
• TESS (Transcription Element Search System)
• MatInspector (Public Domain)

PFAM : Multiple alignments and profile HMMs of protein domains

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Version 7.2 of Pfam (April 2002) contains alignments and models for 3735 protein families, based on the Swissprot 40 and SP-TrEMBL 18 protein sequence databases. It is intended for use with the HMMERSEARCH program in GCG.

• Pfam release notes
• The Pfam site at Washington University, St. Louis
• The Pfam site at the Sanger Centre

Protein motifs database

• The ProSite HomePage at ExPASy

• ACHS
• Get Meduser Account
• Connecting to the MEDUSER Server
• Get SEQWEB Account
• How To Find ITC-ACHS
• Links to PDF Documents

• Molecular Biology Software and Services
• * GCG information
• * Local Databases maintained by ACHS
• * Additional resources for molecular biology and sequence analysis
• * WWW resources for Molecular Biology and Sequence analyses
• * Data and tools for Genome data

• Related Links
• Research Computing Support Center
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