Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.

ABSTRACT:

Unlabelled

Ongoing technological advances in genome sequencing are allowing bacterial genomes to be sequenced at ever-lower cost. However, nearly all of these new techniques concomitantly decrease genome quality, primarily due to the inability of their relatively short read lengths to bridge certain genomic regions, e.g., those containing repeats. Fragmentation of predicted open reading frames (ORFs) is one possible consequence of this decreased quality. In this study we quantify ORF fragmentation in draft microbial genomes and its effect on annotation efficacy, and we propose a solution to ameliorate this problem.

Results

A survey of draft-quality genomes in GenBank revealed that fragmented ORFs comprised > 80% of the predicted ORFs in some genomes, and that increased fragm

SUBMITTER: Klassen JL 

PROVIDER: S-EPMC3322347 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature