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yrGATE specifications

Information


Unique identifier OMICS_23245
Name yrGATE
Alternative name Your Gene structure Annotation Tool for Eukaryotes
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline Volker Brendel

Information


Unique identifier OMICS_23245
Name yrGATE
Alternative name Your Gene structure Annotation Tool for Eukaryotes
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Volker Brendel

Publication for Your Gene structure Annotation Tool for Eukaryotes

yrGATE citations

 (3)
library_books

QTLs and candidate genes for desiccation and abscisic acid content in maize kernels

2010
BMC Plant Biol
PMCID: 2826337
PMID: 20047666
DOI: 10.1186/1471-2229-10-2

[…] had previously been mapped at bins 2.02-2.03, 4.09-4.11 and 5.01 (Génoplante data base, http://urgi.versailles.inra.fr/GnpMap, data not shown) in maize. Nevertheless, only two maize ZEP genes, ZEP1 (yrGATE_Zm2 gZEP1) and ZEP2 (yrGATE_Zm10 gZEP2), were ascertained from our data mining and PCR fragment joining (Additional file ), in agreement with a recent report [], and mapped on IBM mapping panel […]

library_books

MaizeGDB becomes ‘sequence centric’

2009
PMCID: 2964019
PMID: 21847242
DOI: 10.1093/database/bap020

[…] PlantGDB () and made available to the community. Annotation project personnel contact researchers who may be working on particular genes in the list; the researcher annotates the gene directly using yrGATE, the xGDB genome annotation tool (); and that annotation becomes available at both PlantGDB [via the maize xGDB browser called ZmGDB ()] and MaizeGDB, pending approval by project personnel. Ann […]

library_books

Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

2007
BMC Genomics
PMCID: 2077340
PMID: 17880721
DOI: 10.1186/1471-2164-8-330

[…] Gene prediction was done using a combination of ab initio and EST-alignment based methods as previously detailed [,]. Annotation was completed using yrGATE and viewed as part of the xGDB system [,]. A database with annotations was created called GmaxGDB []. Each predicted gene was subjected to a BLASTP query of the NCBI nr database with default pa […]

Citations

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yrGATE institution(s)
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Department of Statistics, Iowa State University, Ames, IA, USA
yrGATE funding source(s)
Supported by the National Science Foundation Plant Genome Research Program grant DBI-0321600.

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