SNAPping Up Functionally Related Genes Based on Context Information: A Colinearity-Free Approach
Computer-assisted functional assignment of gene products traditionally involves identifying a significant resemblance to an experimentally characterized protein or sequence motif. Due to the constant improvement of the sequence comparison techniques, reliable recognition of extremely distant relationships between proteins has become possible. At the same time, further progress in this direction is becoming increasingly difficult, following the rule of diminishing returns — improvements of ever smaller significance require ever growing effort and sophistication. Consequently, the quest to develop complementary, similarity-free computational approaches to elucidate gene function has been triggered. For example, methods based on the linguistic analysis of textual sequence annotation and scientific literature (reviewed in Andrade and Bork 2000) and correlating protein amino acid composition with enzyme nomenclature (des Jardins 1997) have been explored.
KeywordsCarbohydrate Codon Tyrosine Tuberculosis Biodegradation
Unable to display preview. Download preview PDF.
- Felsenstein J (1989) PHYLIP — phylogeny inference package. Cladistics 5: 164–166Google Scholar
- Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27–30Google Scholar
- Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N (1998) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1: 0009Google Scholar
- Tamames J, Casari G, Ouzounis C, Valencia A (1997) Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44:66–73 Watanabe H, Mori H, Itoh T, Gojobori T (1997) Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol 44: S57 — S64Google Scholar