Bioinformatics Links Directory : General Resources

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

A Quick Guide To Sequenced Genomes - (Found June 19, 2008 )

The Quick Guide includes descriptions of more than 150 organisms and has links to sequencing centers and scientific abstracts.
http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml

InterProScan - (Found June 19, 2008 )

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.
http://www.ebi.ac.uk/InterProScan/

ISC Large-scale Sequencing Project Database - (Found June 19, 2008 )

The International Sequencing Consortium (ISC) Large-scale Sequencing Project Database contains information on current and completed sequencing projects, including project timelines, funding agencies, sequencing strategy and links out to project web pages.
http://www.intlgenome.org/viewDatabase.cfm

JCat - (Found June 19, 2008 )

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.
http://www.jcat.de/

MIPS - (Found June 19, 2008 )

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.
http://mips.gsf.de/

NCBI Assembly Archive - (Found June 19, 2008 )

The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive's raw sequence data.
http://www.ncbi.nlm.nih.gov/projects/assembly/

NCBI Taxonomy Database - (Found June 19, 2008 )

Taxonomic classification of all organisms with sequences in GenBank.
http://www.ncbi.nlm.nih.gov/Taxonomy

NEWT - (Found June 19, 2008 )

NEWT is the taxonomy database maintained by the UniProt group.
http://www.ebi.ac.uk/newt/display

PhenomicDB - (Found June 19, 2008 )

PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.
http://www.phenomicdb.de/

iCE - internet Contig Explorer - (Found June 19, 2008 )

Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.
http://ice.bcgsc.bc.ca/