A novel min-cost flow method for estimating transcript expression with RNA-Seq.

ABSTRACT:

Background

Through transcription and alternative splicing, a gene can be transcribed into different RNA sequences (isoforms), depending on the individual, on the tissue the cell is in, or in response to some stimuli. Recent RNA-Seq technology allows for new high-throughput ways for isoform identification and quantification based on short reads, and various methods have been put forward for this non-trivial problem.

Results

In this paper we propose a novel radically different method based on minimum-cost network flows. This has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of

SUBMITTER: Tomescu AI 

PROVIDER: S-EPMC3622638 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature