PASTA: splice junction identification from RNA-Sequencing data

BMC Bioinformatics

Shaojun Tang²  Alberto Riva¹ 

[1] University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA

[2] Current address: Proteomics Center at Children's Hospital Boston, Boston, MA, USA

关键词: Computational analysis of alternative splicing;    Alternative splicing;    Next-generation sequencing;    RNA-Seq;   

Others  :  1087919
DOI  :  10.1186/1471-2105-14-116

 received in 2012-08-13, accepted in 2013-03-19,  发布年份 2013

【 摘 要 】

Background

Next generation transcriptome sequencing (RNA-Seq) is emerging as a powerful experimental tool for the study of alternative splicing and its regulation, but requires ad-hoc analysis methods and tools. PASTA (Patterned Alignments for Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designed for RNA-Seq data, relying on a highly accurate alignment strategy and on a combination of heuristic and statistical methods to identify exon-intron junctions with high accuracy.

Results

Comparisons against TopHat and other splice junction prediction software on real and simulated datasets show that PASTA exhibits high specificity and sensitivity, especially at lower coverage levels. Moreover, PASTA is highly configurable and flexible, and can therefore be applied in a wide range of analysis scenarios: it is able to handle both single-end and paired-end reads, it does not rely on the presence of canonical splicing signals, and it uses organism-specific regression models to accurately identify junctions.

Conclusions

PASTA is a highly efficient and sensitive tool to identify splicing junctions from RNA-Seq data. Compared to similar programs, it has the ability to identify a higher number of real splicing junctions, and provides highly annotated output files containing detailed information about their location and characteristics. Accurate junction data in turn facilitates the reconstruction of the splicing isoforms and the analysis of their expression levels, which will be performed by the remaining modules of the PASTA pipeline, still under development. Use of PASTA can therefore enable the large-scale investigation of transcription and alternative splicing.

【 授权许可】

   
2013 Tang and Riva; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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