Automatically extracting functionally equivalent proteins from SwissProt.

ABSTRACT:

Background

There is a frequent need to obtain sets of functionally equivalent homologous proteins (FEPs) from different species. While it is usually the case that orthology implies functional equivalence, this is not always true; therefore datasets of orthologous proteins are not appropriate. The information relevant to extracting FEPs is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEPs to be extracted on a one-off basis. However there has been no resource allowing the easy, automatic extraction of groups of FEPs - for example, all instances of protein C.We have developed FOSTA, an automatically generated database of FEPs annotated as having the same function in UniProtKB/Swiss-Prot which can be used for large-scale analysis. The me

SUBMITTER: McMillan LE 

PROVIDER: S-EPMC2576269 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature