Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.

ABSTRACT: While most transcriptome analyses in high-throughput clinical studies focus on gene level expression, the existence of alternative isoforms of gene transcripts is a major source of the diversity in the biological functionalities of the human genome. It is, therefore, essential to annotate isoforms of gene transcripts for genome-wide transcriptome studies. Recently developed mRNA sequencing technology presents an unprecedented opportunity to discover new forms of transcripts, and at the same time brings bioinformatic challenges due to its short read length and incomplete coverage for the transcripts. In this work, we proposed a computational approach to reconstruct new mRNA transcripts from short sequencing reads with reference information of known transcripts in existing databases. The pri

SUBMITTER: Seok J 

PROVIDER: S-EPMC3270033 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature