Motivation: An algorithm for comparative analysis of multiple trees reconstructed for representative protein families are discussed. This algorithm is based on the hypotheses of gene loss and horizontal gene transfers and uses stochastic methods and optimization. Some practical results are discussed. We describe a species tree comprising 40 prokaryotic organisms constructed by our algorithm on ...

Extensive genome resources have now been developed for both spruce and pine. However as other technologies develop and costs drop, other resources become feasible. One such resource, not yet available in conifers, is collecting complete cDNA sequences (full length messenger RNA transcripts). We describe our approach for obtaining such sequences and the importance of this resource. Second, exist...

Genomic filtering is a rapid approach to identifying and prioritizing molecular targets for drug discovery. For infectious disease applications, comparative genomics filters allow the selection of pathogen-specific gene products, whereas functional genomics filters, such as RNA interference (RNAi), allow the selection of gene products essential for pathogen survival. The approach is especially ...

MOTIVATION The recent discovery of the first small modulatory RNA (smRNA) presents the challenge of finding other molecules of similar length and conservation level. Unlike short interfering RNA (siRNA) and micro-RNA (miRNA), effective computational and experimental screening methods are not currently known for this species of RNA molecule, and the discovery of the one known example was partly ...

Comparative genomics is essentially a form of data mining in large collections of n-ary relations between genomic elements. Increases in the number of sequenced genomes create a stress on comparative genomics that grows, at worse geometrically, for every increase in sequence data. Even modestly-sized labs now routinely obtain several genomes at a time, and like large consortiums expect to be ab...