Authors:
Michaël Vyverman
1
;
Dieter De Smedt
1
;
Yao-Cheng Lin
2
;
Lieven Sterck
2
;
Bernard De Baets
1
;
Veerle Fack
1
and
Peter Dawyndt
1
Affiliations:
1
Ghent University, Belgium
;
2
VIB and Ghent University, Belgium
Keyword(s):
Spliced Alignment, Splice Site Detection, Read Mapping, Long Reads, cDNA Mapping, RNA-seq.
Related
Ontology
Subjects/Areas/Topics:
Algorithms and Software Tools
;
Bioinformatics
;
Biomedical Engineering
;
Next Generation Sequencing
;
Sequence Analysis
;
Transcriptomics
Abstract:
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.