GOTaxExplorer is a free and easy to use software that presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification.
GOTaxExplorer integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: · selection of sets · comparison of sets of Pfam families · semantic comparison of sets of GO terms · functional comparison of sets of gene products
This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes.
Furthermore, GOTaxExplorer enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms.
The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO.
This method is independent of sequence similarity and therefore capable of finding functionally equivalent or functionally related proteins that are not homologous.
