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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.

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


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 or


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

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