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Fast and accurate cDNA mapping and splice site identification

Boekbijdrage - Boekhoofdstuk Conferentiebijdrage

Mapping and alignment of cDNA sequences containing splice sites is an algorithmically and computationally challenging task. Most recently developed spliced aligners are designed for mapping short reads and sacrifice sensitivity for increased performance. We present mesalina, a highly accurate spliced aligner, that can also be used to detect novel non-canonical splice sites and whose performance is more robust with respect to increasing read length. Mesalina utilizes the seed-extend strategy, combining fast retrieval of maximal exact matches with a sensitive sandwich dynamic programming algorithm. Preliminary results indicate that mesalina is accurate and very fast, especially for mapping longer reads. In particular, it is more than ten times faster than mappers with a comparable accuracy. Mesalina is available from https://github.ugent.be/ComputationalBiology/mesalina.
Boek: BIOINFORMATICS 2014 : proceedings of the international conference on bioinformatics models, methods and algorithms
Pagina's: 233 - 238
Jaar van publicatie:2014