Online Discovery and Refinement of Novel Genes Using GeneScope

We present a novel gene finding and validation tool, called GeneScope, which is capable of finding and validating genes declaratively by autonomously integrating heterogeneous online resources. GeneScope also supports user defined concepts to articulate gene structures, and refine existing concepts toward the discovery of the intended genes. The system relies upon a new string query language called StriQL and the prototype has been implemented using the LifeDB database system. We also report the discovery of two new alternative splice variants of the human telomerase reverse transcriptase (hTERT) gene and their validation using GeneScope. We demonstrate that GeneScopepsilas declarativity now makes it possible for users to engage in large scale and speculative gene discovery with little or no cost. The relatively effortless discovery of the hTERT genes using GeneScope affirms this claim.