TY - JOUR
T1 - PlantGDB
T2 - A resource for comparative plant genomics
AU - Duvick, Jon
AU - Fu, Ann
AU - Muppirala, Usha
AU - Sabharwal, Mukul
AU - Wilkerson, Matthew D.
AU - Lawrence, Carolyn J.
AU - Lushbough, Carol
AU - Brendel, Volker
N1 - Funding Information:
The authors would like to thank Dr. Q. Dong, Dr S.D. Schlueter and Dr B.-B.Wang for their many contributions to PlantGDB over the years, M. Brekke for system support, and the many PlantGDB users who have helped us to improve this resource by providing feedback and suggestions. This work is supported in part by a grant from the National Science Foundation Plant Genome Research Program to V.B., C.J.L, and C.L. (DBI-0606909). Funding to pay the Open Access publication charges for this article was provided by the cited NSF grant.
PY - 2008/1
Y1 - 2008/1
N2 - PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for > 100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.
AB - PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for > 100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.
UR - http://www.scopus.com/inward/record.url?scp=38549166729&partnerID=8YFLogxK
U2 - 10.1093/nar/gkm1041
DO - 10.1093/nar/gkm1041
M3 - Article
C2 - 18063570
AN - SCOPUS:38549166729
SN - 0305-1048
VL - 36
SP - D959-D965
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -