Speaker: Robert Jernigan

Title: Using Sequence & Structure Information to Annotate Gene/Protein Function

Abstract:  BLAST is most commonly to find homologous proteins but the BLOSUM matrices it uses to rate sequence changes does not include enough information about the coevolution between pairs of amino acid residues. We are including these mutations is to create different substitution scorings. The functional Gene Ontology annotations have been compared with the ouput for our method. Using this process, it has been shown that we can assign functions to approximately half of the proteins presently having no known function. The functional relation of these other proteins functional assignments are being compared with the present Gene Annotations.  Many of these are more specific but do not contradict previous assignments.  In some cases we can find reports of experimental validation in two cases. First, we have seen that the protein Q96SN8 produced by our new matrix is functionally and evolutionarily related to Q5VU43 in the formation of a pericentrisomal complex. Second, our matrix has been shown to find proteins annotated for magnesium binding where BLOSUM62 does not. This was done when querying with P09936, which was shown to represent a magnesium binding cluster (PMID: 23095498).