Targeted identification of genomic regions using TAGdb

Marshall, Daniel J., Hayward, Alice, Eales, Dominic, Imelfort, Michael, Stiller, Jiri, Berkman, Paul J., Clark, Terry, McKenzie, Megan, Lai, Kaitao, Duran, Chris, Batley, Jacqueline and Edwards, David (2010) Targeted identification of genomic regions using TAGdb. Plant Methods, 6 19: 1-6. doi:10.1186/1746-4811-6-19

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Author Marshall, Daniel J.
Hayward, Alice
Eales, Dominic
Imelfort, Michael
Stiller, Jiri
Berkman, Paul J.
Clark, Terry
McKenzie, Megan
Lai, Kaitao
Duran, Chris
Batley, Jacqueline
Edwards, David
Title Targeted identification of genomic regions using TAGdb
Journal name Plant Methods   Check publisher's open access policy
ISSN 1746-4811
Publication date 2010-08-20
Sub-type Article (original research)
DOI 10.1186/1746-4811-6-19
Open Access Status DOI
Volume 6
Issue 19
Start page 1
End page 6
Total pages 6
Place of publication London, U.K.
Publisher BioMed Central
Collection year 2011
Language eng
Formatted abstract
Background: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.

Results: We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.
© 2010 Marshall et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keyword Multiple sequence alignment
Multiple sequence alignments
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
Official 2011 Collection
School of Agriculture and Food Sciences
 
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Citation counts: TR Web of Science Citation Count  Cited 18 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 26 times in Scopus Article | Citations
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Created: Wed, 02 Feb 2011, 15:03:40 EST by Dr Alice Hayward on behalf of School of Land, Crop and Food Sciences