OrthoMCL-DB -- querying a comprehensive multi-species collection of ortholog groups
What you can do:
Search for predicted ortholog group from 55 species.
Highlights:
- The OrthoMCL database houses ortholog group predictions for 55 species, including 16 bacterial and 4 archaeal genomes representing phylogenetically diverse lineages, and most currently available complete eukaryotic genomes: 24 unikonts (12 animals, 9 fungi, microsporidium, Dictyostelium, Entamoeba), 4 plants oralgae and 7 apicomplexan parasites.
- OrthoMCL software was 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.
- A total of 511,797 proteins (81.6% of the total dataset) were clustered into 70,388 ortholog groups.
- The ortholog database may be queried based on protein or group accession numbers, keyword descriptions or BLAST similarity.
- Information for ortholog groups includes the phyletic profile, the list of member proteins and a multiple sequence alignment, a statistical summary and graphical view of similarities, and a graphical representation of domain architecture.
- OrthoMCL software, the entire FASTA dataset employed and clustering results are available for download.
- OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species,
Keywords:
- orthology prediction
- predicted orthologs
- predicted ortholog group
- phyletic pattern
- phyletic profile
- phylogeny
- protein domain architectures
- homologous proteins
- gene evolutions
- gene prediction
Literature & Tutorials:
This record last updated: 04-18-2014