Bioinformatics Links Directory : General Resources

The resources listed here include tools and databases for general information on a variety of model organisms.

IBM Genome Annotation Page - (Found June 19, 2008 )

IBM's Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (archae, bacteria, eurkaryotes, and viruses). You can query these annotations at the sequence level as well as searchcompare across genomes.
http://cbcsrv.watson.ibm.com/Annotations/home.html

GOLD: Genomes Online Database - (Found June 19, 2008 )

Up-to-date list of complete and ongoing genome projects.
http://www.genomesonline.org/

Codon Usage Database - (Found June 19, 2008 )

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
http://www.kazusa.or.jp/codon/

CodonO - (Found June 19, 2008 )

CodonO is a method for measuring synonymous codon usage bias within and across genomes.
http://www.sysbio.muohio.edu/CodonO/

dbEST - (Found June 19, 2008 )

Expressed Sequence Tags database; a division of GenBank containing single-pass cDNA sequence reads
http://www.ncbi.nlm.nih.gov/dbEST/index.html

DOE Joint Genome Institute Genome Portal - (Found June 19, 2008 )

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.
http://genome.jgi-psf.org/

Ensembl Genome Browser - (Found June 19, 2008 )

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.
http://www.ensembl.org/

Entrez Genomes - (Found June 19, 2008 )

List of prominent complete genomes with access to BLAST and precomputed conserved domains and protein homologs in complete genome context.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

euGenes: Genomic Information for Eukaryotic Organisms - (Found June 19, 2008 )

Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.
http://iubio.bio.indiana.edu:8089/

GCUA: Graphical Codon Usage Analyser - (Found June 19, 2008 )

Graphical representation of codon bias
http://gcua.schoedl.de