SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads

Genomics
Zhaleh SafikhaniChangiz Eslahchi

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.

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Related Concepts

Programming, Linear
Computer Programs and Programming
Nested Transcripts
Sequence Determinations, RNA
MRNA Differential Display
RNA Isoforms
Gene Expression Profiles
RNA
Computer Software
Variant Surface Glycoproteins, Trypanosoma

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