Bioinformatics: Difference between revisions

Revision as of 19:27, 8 February 2008

BioCocoa is an open source Cocoa framework for bioinformatics written in Objective-C

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

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

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

@@ Line 43: / Line 43: @@
 ==Miscellaneous==
-[http://www.gene-regulation.com/ Gene Regulation] - list of resources
+*[http://www.gene-regulation.com/ Gene Regulation] - list of resources
+*[irc://irc.freenode.net/#bioinformatics Bioinformatics IRC channel]