Bioinformatics

On OWW you can find bioinformatics sub-wikis:


 * Wikiomics general bioinformatics wiki
 * Tregwiki gene regulation wiki

For questions use:
 * Bioinformatics Discussion Group

=Bioinformatics links=

Software

 * PFAAT - Protein Family Alignment Annotation Tool

Frameworks

 * BioCocoa is an open source Cocoa framework for bioinformatics written in Objective-C

Online services

 * Biological web services - Taverna Project
 * WebLogo - create sequence logos
 * T-COFFEE server
 * MAFFT: A Program for Multiple Sequence Alignment
 * Block WWW Server
 * SIFT Sorting Intolerant From Tolerant - will return predictions for what amino acid substitutions will affect protein function
 * CODDLE Codons Optimized to Discover Deleterious Lesions - will identify regions of a gene where mutations are likely to be deleterious
 * Regulatory Sequence Analysis Tools (RSAT) provide a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences
 * Superfamily - HMM library and genome assignments server
 * Genome Projector a searchable database browser with zoomable user interface using Google Map API (genome and pathway viewer)

Synthetic biology

 * Synthetic biology tools @ OpenWetWare
 * GeneDesign &beta;2.0
 * Gene Re-design Software Collection by EvolvingCode Group @ UMBC

Databases

 * Entrez cross-database search
 * ExPASy Proteomics Server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
 * UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR
 * DIP catalogs experimentally determined interactions between proteins, it combines information from a variety of sources to create a single, consistent set of protein-protein interactions
 * KEGG: Kyoto Encyclopedia of Genes and Genomes
 * BIND - Biomolecular Interaction Network Database
 * SCOP: Structural Classification of Proteins
 * InterProScan: sequence search
 * Pfam search
 * PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs
 * PRINTS is a compendium of protein fingerprints
 * MetaBase is a user-contributed list of all the biological databases available on the internet

Kinases

 * MAP Kinase Resource
 * Protein Kinase Resource
 * KinG: Kinases in Genomes is a comprehensive collection of Ser/Thr/Tyr specific protein kinases and similar sequences encoded in the completed genomes of eukaryotes and prokaryotes

Miscellaneous
=Bioinformaticians on OpenWetWare=
 * Gene Regulation - list of resources
 * Bioinformatics IRC channel