Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

ABSTRACT: Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Addition

SUBMITTER: Watanabe KA 

PROVIDER: S-EPMC4596398 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature