Bioinformatics: Difference between revisions
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[[Bioinformatics Discussion Group]] | On OWW you can find bioinformatics sub-wikis: | ||
* [[Wikiomics]] general bioinformatics wiki | |||
* [[Tregwiki]] gene regulation wiki | |||
For questions use: | |||
* [[Bioinformatics Discussion Group]] | |||
=Bioinformatics links= | |||
==Software== | ==Software== | ||
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*[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://supfam.org/SUPERFAMILY/ Superfamily] - HMM library and genome assignments server | ||
*[http://www.g-language.org/GenomeProjector/ Genome Projector] a searchable database browser with zoomable user interface using Google Map API (genome and pathway viewer) | |||
===Synthetic biology=== | ===Synthetic biology=== | ||
*[[Synthetic_Biology:Tools|Synthetic biology tools]] @ OpenWetWare | |||
*[http://slam.bs.jhmi.edu/gd/ GeneDesign β2.0] | *[http://slam.bs.jhmi.edu/gd/ GeneDesign β2.0] | ||
*[http://www.evolvingcode.net/codon/ Gene Re-design Software Collection] by EvolvingCode Group @ UMBC | *[http://www.evolvingcode.net/codon/ Gene Re-design Software Collection] by EvolvingCode Group @ UMBC | ||
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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 | ||
*[http://biodatabase.org/ MetaBase] is a user-contributed list of all the biological databases available on the internet | |||
====Kinases==== | ====Kinases==== | ||
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==Miscellaneous== | ==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] | |||
=Bioinformaticians on OpenWetWare= | |||
* [[Category:Bioinformaticians]] | |||
Latest revision as of 05:22, 19 June 2008
On OWW you can find bioinformatics sub-wikis:
For questions use:
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
- 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
- Synthetic biology tools @ OpenWetWare
- GeneDesign β2.0
- Gene Re-design Software Collection by EvolvingCode Group @ UMBC
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
- 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
- Bioinformatics IRC channel
