Bioinformatics

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On OWW you can find bioinformatics sub-wikis:

For questions use:


Contents

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

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

Miscellaneous

Bioinformaticians on OpenWetWare

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