OrthoMCL-DB

You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.

Link/URL:	http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi
What:
Who:	Univ. of Pennsylvania
Updates:
Upcoming events:
Web Services:
edit table

See Help:Database_table for how to add or edit information in this section of EcoliWiki.

About OrthoMCL-DB

OrthoMCL-DB is an orthology database. The OrthoMCL tool is also used by other groups including P-POD.

Content

OrthoMCL DB houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages. OrthoMCL software is used to cluster proteins based on sequence similarity, using an all-against-all BLAST search of each species' proteome, followed by normalization of inter-species differences, and Markov clustering. OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species.

Using OrthoMCL-DB

Usage examples

Add links to additional pages describing success stories here.

Technology

Snipped from http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=orthomcl#Software

 To satisfy the request to run ortholog clustering without depositing data into GUS database, the
 stand-alone version of OrthoMCL was developed as a stand-alone PERL package, which is available at 
 http://orthomcl.cbil.upenn.edu/ORTHOMCL/.

 Stand-alone OrthoMCL requires protein FASTA files for each genomes, and it calls for an 
 all-against-all BLAST analysis. Alternatively, OrthoMCL can start analysis by reading a BPO file 
 (Blast Parsing Out) which describes genes paired by BLAST matches, the E-value, and the identity 
 percentage and the related HSP information.
 
 As a perl package stand-alone OrthoMCL doesn't need compilation. However it requires some softwares 
 and perl modules to run:
    Softwares: 1. BLAST (NCBI-BLAST, WU-BLAST, etc.) 2. MCL (Markov Clustering algorithm), available
    at http://micans.org/mcl/;
    Perl Modules: 1. Bio::SearchIO (part of BioPerl, http://bioperl.org) 2. Storable 

External Links

OrthoMCL-DB URL:http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi

References

See Help:References for how to manage references in EcoliWiki.