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.
KeywordsBasic Local Alignment Search Tool Functional Coupling Query Gene Carbohydrate Utilization Pathway Coefficient
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