FOSTA is a method for identifying functionally equivalent orthologues. It uses sequence information and functional annotations from Swissprot.
FOSTA first identifies all sequence homologues with a BLAST search against Swissprot (v53.0) using an e-value threshold of 10-2. It then removes all paralogues using a functional filter where Swissprot annotations are compared. Finally, it chooses the best functional match from each species to identify the functionally equivalent protein in each species.
To see all the functionally equivalent orthologues for a particular Swissprot ID, enter it in the form on the right. Select what kind of proteins you are interested in. For example, if you don't want to return fragmented proteins, de-select 'Sequence fragments'. 'Unreliable proteins' have been described as hypothetical, probable, putative, -like, or as a homolog of another protein by Swissprot. By de-selecting 'Sequence matches', any assignments made on the basis of sequence matching are eliminated from the results displayed.
Data for each family are available in plain text format. Use the 'Export plain text' button on each page.
The FOSTA paper has been published by BMC Bioinformatics.