Bioinformatics: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
m (Bioinformaticians)
 
(15 intermediate revisions by 2 users not shown)
Line 1: Line 1:
[[Bioinformatics Discussion Group]]
On OWW you can find bioinformatics sub-wikis:


===Software===
* [[Wikiomics]] general bioinformatics wiki
* [[Tregwiki]] gene regulation wiki
 
For questions use:
* [[Bioinformatics Discussion Group]]
 
 
 
=Bioinformatics links=
 
==Software==
*[http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool
*[http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool


====Frameworks====
===Frameworks===
*[http://www.bioinformatics.org/biococoa/ BioCocoa] is an open source Cocoa framework for bioinformatics written in Objective-C
*[http://www.bioinformatics.org/biococoa/ BioCocoa] is an open source Cocoa framework for bioinformatics written in Objective-C


===Online services===
==Online services==
*[http://taverna.sourceforge.net/index.php?doc=services.html Biological web services] - Taverna Project
*[http://taverna.sourceforge.net/index.php?doc=services.html Biological web services] - Taverna Project
*[http://weblogo.berkeley.edu/logo.cgi WebLogo] - create sequence logos
*[http://weblogo.berkeley.edu/logo.cgi WebLogo] - create sequence logos
Line 15: Line 25:
**[http://blocks.fhcrc.org/sift/SIFT.html SIFT] Sorting Intolerant From Tolerant - will return predictions for what amino acid substitutions will affect protein function
**[http://blocks.fhcrc.org/sift/SIFT.html SIFT] Sorting Intolerant From Tolerant - will return predictions for what amino acid substitutions will affect protein function
**[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://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: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
===Databases===
*[http://www.ncbi.nlm.nih.gov/Entrez/ Entrez] cross-database search
*[http://expasy.org/ ExPASy Proteomics Server] is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
*[http://www.uniprot.org/ 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
*[http://dip.doe-mbi.ucla.edu/ 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
*[http://www.genome.ad.jp/kegg/ KEGG]: Kyoto Encyclopedia of Genes and Genomes
*[http://www.bind.ca/Action BIND] - Biomolecular Interaction Network Database
*[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
*[http://biodatabase.org/ MetaBase] is a user-contributed list of all the biological databases available on the internet
====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==
*[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
    • 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
  • Genome Projector a searchable database browser with zoomable user interface using Google Map API (genome and pathway viewer)

Synthetic biology

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

Miscellaneous

Bioinformaticians on OpenWetWare

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Bioinformatics&oldid=213602"