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SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data.
- Source :
-
Computer Methods & Programs in Biomedicine . Apr2015, Vol. 119 Issue 1, p53-62. 10p. - Publication Year :
- 2015
-
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 . [ABSTRACT FROM AUTHOR]
- Subjects :
- *INTRONS
*GENETIC regulation
*RNA sequencing
*EXONS (Genetics)
*DATA analysis
Subjects
Details
- Language :
- English
- ISSN :
- 01692607
- Volume :
- 119
- Issue :
- 1
- Database :
- Academic Search Index
- Journal :
- Computer Methods & Programs in Biomedicine
- Publication Type :
- Academic Journal
- Accession number :
- 101918332
- Full Text :
- https://doi.org/10.1016/j.cmpb.2015.02.004