Proteome-wide Analysis

Since the completion of the human genome project, there has been a concerted effort to find all the functional genome sequences and use this knowledge to improve the health of an individual. One such effort concerns the comparative analysis of genomes [Hardison,2003]. One such comparative analysis utilizes a phylogenetic tree to assign functions genome wide [Pellegrini,1999]. This analysis has yielded considerable insight into basic genomic features. For example, observations drawn from comparing mammalian genomes suggest that large sections of the mammalian chromosome have a tendency to change through one of several processes including single nucleotide substitution, transposon insertion and recombination [Mouse,2002]. Likewise, the comparison between Human, Old World and New World monkeys has also been used to capture common mammalian and primate-specific functional elements in the human genome [Boffelli,2003].

Proteomics Analysis

Our work considers genome-wide characterization of physio-chemical proteins that can be attribued to a particular protein function. Specifically, we apply a generalized feature representation of a protein sequence proven successful in previous work [8]. We show that this protocol is superior to sequence analysis techniques, e.g. blast and find that it captures (arguably) more accurate evolutionary relationships between organisms than standard sequence-analysis techniques.