OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds

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OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds

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Title: OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds
Author(s):
Wu, Jie;
Anczuk©w, Olga;
Krainer, Adrian R.;
Zhang, Michael Q.;
Zhang, Chaolin
Date Created: 2013-04
Item Type: Article
Keywords: Exons (Genetics)
Genetic algorithms--OLego
RNA splicing
Messenger RNA
Description: Includes supplementary materials and data.
Abstract: A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (∼14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.;
Publisher: Oxford University Press
ISSN: 1362-4962
Source: Nucleic Acids Research
Link to Related Resource: http://dx.doi.org/10.1093/nar/gkt216
Persistent Link: http://hdl.handle.net/10735.1/3938
Bibliographic Citation: Wu, Jie, Olga Anczuków, Adrian R. Krainer, Michael Q. Zhang, et al. 2013. "OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds." Nucleic Acids Research 41(10): 5149-5163.
Terms of Use: CC BY-NC 3.0 (Attribution--Non-Commercial)
©2013 The Authors. Published by Oxford University Press

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CC BY-NC 3.0 (Attribution--Non-Commercial) Except where otherwise noted, this item's license is described as CC BY-NC 3.0 (Attribution--Non-Commercial)