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Parametric Alignment of Drosophila Genomes
2006
PLoS Computational Biology
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces which are suitable for Needleman--Wunsch alignment. In these alignment methods, it is standard practice to fix the parameters and to produce a single
doi:10.1371/journal.pcbi.0020073
pmid:16789815
pmcid:PMC1480539
fatcat:qrq66ady25aelhsaakfpgyqqyq