TrueSight

Self-training algorithm for splice junction detection using RNA-seq

Yang Li, Hong Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. However, due to the limited read length of NGS data, it is extremely challenging to accurately map RNA-seq reads to splice junctions, which is critically important for the analysis of alternative splicing and isoform construction. Several tools have been developed to find splice junctions by RNA-seq de novo, without the aid of gene annotations [1-3]. However, the sensitivity and specificity of these tools need to be improved. In this paper, we describe a novel method, called TrueSight, that combines information from (i) RNA-seq read mapping quality and (ii) coding potential from the reference genome sequences into a unified model that utilizes semi-supervised learning to precisely identify splice junctions.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings
Pages163-164
Number of pages2
DOIs
StatePublished - May 15 2012
Event16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012 - Barcelona, Spain
Duration: Apr 21 2012Apr 24 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7262 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012
CountrySpain
CityBarcelona
Period4/21/124/24/12

Fingerprint

Training Algorithm
RNA
Sequencing
Alternative Splicing
Semi-supervised Learning
Profiling
Specificity
Annotation
Genome
Coding
Genes
Gene
Supervised learning
Model

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Li, Y., Li, H. M., Burns, P., Borodovsky, M., Robinson, G. E., & Ma, J. (2012). TrueSight: Self-training algorithm for splice junction detection using RNA-seq. In Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings (pp. 163-164). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7262 LNBI). https://doi.org/10.1007/978-3-642-29627-7_14

TrueSight : Self-training algorithm for splice junction detection using RNA-seq. / Li, Yang; Li, Hong Mei; Burns, Paul; Borodovsky, Mark; Robinson, Gene E.; Ma, Jian.

Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. p. 163-164 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7262 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Li, Y, Li, HM, Burns, P, Borodovsky, M, Robinson, GE & Ma, J 2012, TrueSight: Self-training algorithm for splice junction detection using RNA-seq. in Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 7262 LNBI, pp. 163-164, 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, 4/21/12. https://doi.org/10.1007/978-3-642-29627-7_14
Li Y, Li HM, Burns P, Borodovsky M, Robinson GE, Ma J. TrueSight: Self-training algorithm for splice junction detection using RNA-seq. In Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. p. 163-164. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-29627-7_14
Li, Yang ; Li, Hong Mei ; Burns, Paul ; Borodovsky, Mark ; Robinson, Gene E. ; Ma, Jian. / TrueSight : Self-training algorithm for splice junction detection using RNA-seq. Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. 2012. pp. 163-164 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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