Bioinformatics: Difference between revisions
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*[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://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 | *[http://bioinf.man.ac.uk/dbbrowser/PRINTS/ PRINTS] is a compendium of protein fingerprints | ||
====Kinases==== | |||
*[http://mapk.8m.com/ MAP Kinase Resource] | |||
*[http://www.kinasenet.org/pkr/Welcome.do Protein Kinase Resource] | |||
*[http://hodgkin.mbu.iisc.ernet.in/~king/ 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== | ==Miscellaneous== | ||
[http://www.gene-regulation.com/ Gene Regulation] - list of resources | [http://www.gene-regulation.com/ Gene Regulation] - list of resources | ||
Revision as of 11:35, 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
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
