Bioinformatics: Difference between revisions
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**[http://www.proweb.org/coddle/ CODDLE] Codons Optimized to Discover Deleterious Lesions - will identify regions of a gene where mutations are likely to be deleterious | **[http://www.proweb.org/coddle/ CODDLE] Codons Optimized to Discover Deleterious Lesions - will identify regions of a gene where mutations are likely to be deleterious | ||
*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools (RSAT)] provide a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences | *[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools (RSAT)] provide a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences | ||
*[http://supfam.org/SUPERFAMILY/ Superfamily] - HMM library and genome assignments server | |||
*[http://slam.bs.jhmi.edu/gd/ GeneDesign β2.0] | *[http://slam.bs.jhmi.edu/gd/ GeneDesign β2.0] | ||
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*[http://www.bind.ca/Action BIND] - Biomolecular Interaction Network Database | *[http://www.bind.ca/Action BIND] - Biomolecular Interaction Network Database | ||
*[http://scop.berkeley.edu/ SCOP]: Structural Classification of Proteins | *[http://scop.berkeley.edu/ SCOP]: Structural Classification of Proteins | ||
*[http://www.ebi.ac.uk/InterProScan/ InterProScan]: sequence search | |||
*[http://www.sanger.ac.uk/Software/Pfam/search.shtml Pfam search] | |||
*[http://expasy.org/prosite/ 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 | |||
*[http://bioinf.man.ac.uk/dbbrowser/PRINTS/ PRINTS] is a compendium of protein fingerprints | |||
Revision as of 11:17, 8 September 2006
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
- 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
- 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
- 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
