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• W2167436707 abstract "We present a pairwise local aligner, FEAST, which uses two new techniques: a sensitive extension algorithm for identifying homologous subsequences, and a descriptive probabilistic alignment model. We also present a new procedure for training alignment parameters and apply it to the human and mouse genomes, producing a better parameter set for these sequences. Our extension algorithm identifies homologous subsequences by considering all evolutionary histories. It has higher maximum sensitivity than Viterbi extensions, and better balances specificity. We model alignments with several submodels, each with unique statistical properties, describing strongly similar and weakly similar regions of homologous DNA. Training parameters using two submodels produces superior alignments, even when we align with only the parameters from the weaker submodel. Our extension algorithm combined with our new parameter set achieves sensitivity 0.59 on synthetic tests. In contrast, LASTZ with default settings achieves sensitivity 0.35 with the same false positive rate. Using the weak submodel as parameters for LASTZ increases its sensitivity to 0.59 with high error. FEAST is available at http://monod.uwaterloo.ca/feast/." @default.
• W2167436707 created "2016-06-24" @default.
• W2167436707 creator A5012818010 @default.
• W2167436707 creator A5070259161 @default.
• W2167436707 date "2011-05-01" @default.
• W2167436707 modified "2023-09-23" @default.
• W2167436707 title "FEAST: Sensitive Local Alignment with Multiple Rates of Evolution" @default.
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• W2167436707 doi "https://doi.org/10.1109/tcbb.2010.76" @default.
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