Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.

ABSTRACT:

Background

Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes.

Results

Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular frac

SUBMITTER: Guillot L 

PROVIDER: S-EPMC6337836 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature