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Comput Methods Programs Biomed. 2015 Apr;119(1):53-62. doi: 10.1016/j.cmpb.2015.02.004. Epub 2015 Feb 14.

SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

Author information

1
Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China. Electronic address: johnsunx1@gmail.com.
2
College of Information Engineering, Taishan Medical University, Taian, Shandong 271000, China.
3
Department of Biomedical Informatics, Windber Research Institute, Windber, PA 15963, USA.
4
Applied Statistics Center, Columbia University, New York, NY 10027, USA.
5
Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhua West Road, Jinan, Shandong 250011, China.
6
Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.

Abstract

Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html.

KEYWORDS:

Gene-scale annotation; Genome-scale annotation; R package; Splicing junction

PMID:
25720307
DOI:
10.1016/j.cmpb.2015.02.004
[Indexed for MEDLINE]

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