Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

ABSTRACT:

Background

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded.

Methodology

We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgu

SUBMITTER: Kuroshu RM 

PROVIDER: S-EPMC2866332 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature