Recent advances in the sequencing technologies have provided a handful of RNA-seq datasets for transcriptome analysis. However, reconstruction of full-length isoforms and estimation of the expression level of transcripts with a low cost is a challenging task. Researchers at the University of Tehran, Iran propose a novel de novo method named SSP that incorporate Interval Integer Linear Programming to resolve alternatively spliced isoforms and reconstruct the whole transcriptome from short reads. Experimental results show that SSP is fast and precise in determining different alternatively spliced isoforms along with the estimation of reconstructed transcripts abundances.
Availability – SSP software package is available at http://www.bioinf.cs.ipm.ir/software/ssp
- Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C. (2013) SSP: An interval integer linear programming for De novo transcriptome assembly and isoform discovery of RNA-seq reads. Genomics [Epub ahead of print]. [abstract]