UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.

ABSTRACT: Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better performance compared with earlier developed algorithms such as TopHat and MapSplice. To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA. This line of research led to yet another new algorithm, UnSplicer, designed for eukaryotic species with compact genomes where functional alternative splicing is likely to be dominated by splicing noise. Genome-specific parameters of the new algorithm are ge

SUBMITTER: Burns PD 

PROVIDER: S-EPMC3936741 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature