MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

Campbell, M. S., Law, M., Holt, C., Stein, J. C., Moghe, G. D., Hufnagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S. H., Childs, K. L., Sun, Y., Jiang, N., Yandell, M. (February 2014) MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations. Plant Physiol, 164 (2). pp. 513-24. ISSN 0032-0889

URL: http://www.ncbi.nlm.nih.gov/pubmed/24306534
DOI: 10.1104/pp.113.230144

Abstract

We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
organism description > plant
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: February 2014
Date Deposited: 21 Feb 2014 21:35
Last Modified: 21 Feb 2014 21:35
PMCID: PMC3912085
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29544

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving