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Fast and accurate cDNA mapping and splice site identification

Michaël Vyverman (UGent) , Dieter De Smedt, Yao-Cheng Lin (UGent) , Lieven Sterck (UGent) , Bernard De Baets (UGent) , Veerle Fack (UGent) and Peter Dawyndt (UGent)
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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.
Keywords
RNA-seq, cDNA Mapping, Long Reads, Read Mapping, Splice Site Detection, READS, RNA-SEQ, JUNCTIONS, SUFFIX ARRAYS, ALIGNMENT, Spliced Alignment

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MLA
Vyverman, Michaël et al. “Fast and Accurate cDNA Mapping and Splice Site Identification.” BIOINFORMATICS 2014 : Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Ed. O Pastor et al. Setubal, Portugal: Scitepress, 2014. 233–238. Print.
APA
Vyverman, M., De Smedt, D., Lin, Y.-C., Sterck, L., De Baets, B., Fack, V., & Dawyndt, P. (2014). Fast and accurate cDNA mapping and splice site identification. In O. Pastor, C. Sinoquet, G. Plantier, T. Schultz, A. Fred, & G. Gamboa (Eds.), BIOINFORMATICS 2014 : proceedings of the international conference on bioinformatics models, methods and algorithms (pp. 233–238). Presented at the 5th International conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS) ; part of 7th International joint conference on Biomedical Engineering Systems and Technologies (BIOSTEC), Setubal, Portugal: Scitepress.
Chicago author-date
Vyverman, Michaël, Dieter De Smedt, Yao-Cheng Lin, Lieven Sterck, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2014. “Fast and Accurate cDNA Mapping and Splice Site Identification.” In BIOINFORMATICS 2014 : Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, ed. O Pastor, C Sinoquet, G Plantier, T Schultz, A Fred, and G Gamboa, 233–238. Setubal, Portugal: Scitepress.
Chicago author-date (all authors)
Vyverman, Michaël, Dieter De Smedt, Yao-Cheng Lin, Lieven Sterck, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2014. “Fast and Accurate cDNA Mapping and Splice Site Identification.” In BIOINFORMATICS 2014 : Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, ed. O Pastor, C Sinoquet, G Plantier, T Schultz, A Fred, and G Gamboa, 233–238. Setubal, Portugal: Scitepress.
Vancouver
1.
Vyverman M, De Smedt D, Lin Y-C, Sterck L, De Baets B, Fack V, et al. Fast and accurate cDNA mapping and splice site identification. In: Pastor O, Sinoquet C, Plantier G, Schultz T, Fred A, Gamboa G, editors. BIOINFORMATICS 2014 : proceedings of the international conference on bioinformatics models, methods and algorithms. Setubal, Portugal: Scitepress; 2014. p. 233–8.
IEEE
[1]
M. Vyverman et al., “Fast and accurate cDNA mapping and splice site identification,” in BIOINFORMATICS 2014 : proceedings of the international conference on bioinformatics models, methods and algorithms, Angers, France, 2014, pp. 233–238.
@inproceedings{6851320,
  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.},
  author       = {Vyverman, Michaël and De Smedt, Dieter and Lin, Yao-Cheng and Sterck, Lieven and De Baets, Bernard and Fack, Veerle and Dawyndt, Peter},
  booktitle    = {BIOINFORMATICS 2014 : proceedings of the international conference on bioinformatics models, methods and algorithms},
  editor       = {Pastor, O and Sinoquet, C and Plantier, G and Schultz, T and Fred, A and Gamboa, G},
  isbn         = {9789897580123},
  keywords     = {RNA-seq,cDNA Mapping,Long Reads,Read Mapping,Splice Site Detection,READS,RNA-SEQ,JUNCTIONS,SUFFIX ARRAYS,ALIGNMENT,Spliced Alignment},
  language     = {eng},
  location     = {Angers, France},
  pages        = {233--238},
  publisher    = {Scitepress},
  title        = {Fast and accurate cDNA mapping and splice site identification},
  url          = {http://dx.doi.org/10.5220/0004903502330238},
  year         = {2014},
}

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