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Component 2 of the BayGenomics project is led by Drs. Patricia Babbitt and Thomas Ferrin. Its goal is to analyze the sequences of the genes that have been trapped within Component 1 by developing and applying bioinformatics protocols to store, annotate, and evaluate the gene-trap sequences. Gene-trap sequnces are screened for roles in cardiopulmonary function by comparing them to databases of sequences/genetic markers known to have relevant functions. To functionally characterize gene-trap sequences of potential relevance, we use family and superfamily analysis to (1) add to functional definitions of sequences that have already been characterized or that have close homologues with known function, (2) characterize Open Reading Frames (ORFs) whose only close homologues are of unknown function, and (3) characterize ORFs with only distantly related homologues. ORFs with no identifiable homologues in the databases are evaluated for structural and functional characteristics using pattern- and motif-finding algorithms. Data generated are to be integrated with the GenMAPP project and the experimental efforts.
The members of the BayGenomics bioinformatics group are Conrad Huang, Doug Stryke, Michiko Kawamoto, Susan Johns, Courtney Harper, Roy Lee, Elaine Meng, Scooter Morris, and Patricia Chang.