title: SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.
abstract: 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 are challenging tasks. We propose a novel de novo method named SSP that incorporates 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 transcript abundances. The SSP software package is available at http://www.bioinf.cs.ipm.ir/software/ssp.
authors.affiliation: Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Zhaleh
authors.initials: Z
authors.lastname: Safikhani
authors.affiliation: National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran. Electronic address: sadeghi@nigeb.ac.ir.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
authors.affiliation: School of Mathematics, Statistics and Computer Sciences, Center of Excellence in Biomathematics, College of Science, University of Tehran, Tehran, Iran.
authors.forename: Hamid
authors.initials: H
authors.lastname: Pezeshk
authors.affiliation: Department of Computer Science, Shahid Beheshti University, GC., Tehran, Iran; School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
authors.forename: Changiz
authors.initials: C
authors.lastname: Eslahchi
mesh_terms: D017398:Alternative Splicing; D020869:Gene Expression Profiling / Q000379:methods; D011382:Programming, Linear / Q000191:economics; D059368:RNA Isoforms / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000191:economics / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D059368:RNA Isoforms
keywords: Alternative splicing; Isoforms; Linear programming; RNA sequencing; Transcriptome