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 β2.0
• 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

• Gene Regulation - list of resources
• Bioinformatics IRC channel