Bioinformatics

Bioinformatics Discussion Group

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
• GeneDesign β2.0

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