EraGen will develop a new functional genomics software suite that helps scientists use genomic sequence data to solve biological and biomedical problems in this Phase II period. The product will take the scientist beyond classical approaches to sequence annotation, which use BLAST searches to identify homologs, and assume that two proteins related by common ancestry must have analogous functions. The Phase I period demonstrated that this approach to database annotation is often misleading, and frequently misses meaningful interpretations in metazoan proteins. The Phase II period will refine and fully develop the software initiated in Phase I. This software will serve to identify where function might have changed during divergence of a sequence family, and also where recruitment of function has occurred using rates of change from the DNA sequence. In addition, the tools to exploit probabilistic ancestral sequences for both protein/protein and DNA/protein alignments will be fully developed. These tools will detect distant homologs, identify errors across sequence databases, and augment current approaches to gene finding.
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