DNA databases

Protein databases

Species-specific databases

Locus-specific databases

DNA databases

Entrez is the gateway to six major searchable databases of; nucleotides, proteins, 3-D structures, genomes, taxonomy and literature (PubMed). The Genomes database includes the complete genomes of 15 organisms, and chromosome maps of Drosophila, C. elegans, mouse and all human chromosomes. Searching is simple and detailed help is available

The Genome Database contains all of the genomic mapping data from the Human Genome Project. Includes descriptions of regions of the genome (genes, clones, fragile sites etc.), maps of the human genome, and mutations and polymorphisms.

GenBank , the NIH genetic sequence database, provides an annotated, fully searchable collection of all publicly available DNA sequences. GenBank coordinates all sequence information on a daily basis with the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL). You may search Genbank via Entrez or BLAST. You may also submit sequence datato GenBank via the WWW.

BLAST searches all available sequence databases for sequence similarity (homology, identity) with both nucleotide and protein sequences. By searching for local alignments, BLAST can detect similarity in isolated regions of a sequence. There are a number of programs, but to start just paste your sequence into the basic BLAST box and hit submit. Good FAQs available.

Online Mendelian Inheritance in Man database. A catalog of human genes and genetic disorders, and includes information about specific genes that is extensively referenced, images of clinical phenotypes, and other relevant database links. An excellent place to begin to learn about a specific disease gene of interest.

Protein databases

The Protein Databank is an archive of three-dimensional structures of biological macromolecules. Can be searched by journal citation, compound, formula etc. Contains primary and secondary structure information, and crystallographic and NMR experimental data.

The OWL database is a non-redundant protein sequence database that incorporates the SWISSPROT, PIR (1-3), GenBank (translations) and NRL-3D databases. Includes some pictures.

Species-specific databases

Non-redundant B. subtilis Database This joint French-Japanese project provides a set of Bacillus subtilis DNA sequences in which duplications have been removed, and overlaps used to form contigs where possible, searchable by sequence, accession number or text.

Encyclopedia of Drosophila integrates data from the Berkeley Drosophila Genome Project and the Flybase at Indiana University. Multiple search options. Current, containing both published and unpublished data.

The TBASE (Transgenic/Targeted Mutation Database) at the John Hopkins Uni School of Medicine is compiling information on transgenic animals and targeted mutations. It includes unpublished information, some of which may only ever be available on this database.

Locus-specific mutation databases

Cystic Fibrosis Mutation Database. A non-searchable list of CFTR mutations. Also CFTR sequence data (DNA, cDNA and polymorphisms).

Emery-Dreifuss Muscular Dystrophy Mutation Database. A non-searchable list of EMD mutations.

Hemophilia A Mutation Database. A searchable database that also has text on the molecular pathology of this disorder and sequence data.

The PAX6 Mutation Database This database is searchable by the property of the mutation (eg location, type, inheritance).

End of Biomed Resources

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