Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome.

ABSTRACT:

Background

Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure.

Methodology

We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derived from the fungus Laccaria bicolor, which develops a mycorrhizal symbiot

SUBMITTER: Larsen PE 

PROVIDER: S-EPMC2897884 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature