OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
Open accessAbstract
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.
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Confounders do not account for the differential splicing signal; it was reproduced with an alternative pipeline and validated with RT-PCR.
“We confirmed that confounders do not account for the differential splicing signal, reproduced the global differential splicing signal with an alternative pipeline15, and performed technical validation with RT–PCR (Extended Data Figs 4d–g, 5a), confirming the differential splicing analysis.”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [15]
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“Briefly, we first performed de novo mapping of raw reads to the reference genome (mm9), as well as known and novel exon junctions using small seeds with the OLego algorithm (Wu et al., 2013).”
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“Reads in each dataset were mapped to the mouse (mm10) or human (hg19) genome by OLego (http://zhanglab.c2b2.columbia.edu/index.php/OLego) (Wu et al., 2013) with 14-nt non-overlapping seeds, requiring ≤ 3 mismatches per read.”
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Self-citation
- Authors
- Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q., & Zhang, C.
- Affiliations
- Cold Spring Harbor Laboratory (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Zhang, Michael Q.
- Zhang, Chaolin
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-04-08
- Volume
- 41
- Issue
- 10
- Pages
- 5149-5163
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3664805
- OpenAlex
- W2112813983
- Cited by
- 123
- References
- 43
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 6 · 2023: 2 · 2022: 3 · 2021: 19 · 2020: 10 · 2019: 9 · 2018: 15 · 2017: 10 · 2016: 10 · 2015: 12 · 2014: 12 · 2013: 2
- FWCI
- 5.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Funders
- National Institutes of Health
- National Key Research and Development Program of China (2012CB316503)
- National Institute of General Medical Sciences (GM74688, K99GM095713, R01GM074688, R00GM095713)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- mRNA-seq, small seeds, Burrows-Wheeler transform, splice site strength, intron size, novel exons, mouse transcriptome
- MeSH terms
- Algorithms, Animals, Chromosome Mapping, Exons, Mice, Inbred C57BL, Retina, RNA Splicing, RNA, Messenger, Software, Sequence Alignment, Genome, Sequence Analysis, RNA, Gene Expression Profiling, RNA Splice Sites, Mice
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