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CMD: a Cotton Microsatellite Database resource for Gossypium genomics

BACKGROUND: The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains pub...

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Autores principales: Blenda, Anna, Scheffler, Jodi, Scheffler, Brian, Palmer, Michael, Lacape, Jean-Marc, Yu, John Z, Jesudurai, Christopher, Jung, Sook, Muthukumar, Sriram, Yellambalase, Preetham, Ficklin, Stephen, Staton, Margaret, Eshelman, Robert, Ulloa, Mauricio, Saha, Sukumar, Burr, Ben, Liu, Shaolin, Zhang, Tianzhen, Fang, Deqiu, Pepper, Alan, Kumpatla, Siva, Jacobs, John, Tomkins, Jeff, Cantrell, Roy, Main, Dorrie
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539020/
https://www.ncbi.nlm.nih.gov/pubmed/16737546
http://dx.doi.org/10.1186/1471-2164-7-132
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author Blenda, Anna
Scheffler, Jodi
Scheffler, Brian
Palmer, Michael
Lacape, Jean-Marc
Yu, John Z
Jesudurai, Christopher
Jung, Sook
Muthukumar, Sriram
Yellambalase, Preetham
Ficklin, Stephen
Staton, Margaret
Eshelman, Robert
Ulloa, Mauricio
Saha, Sukumar
Burr, Ben
Liu, Shaolin
Zhang, Tianzhen
Fang, Deqiu
Pepper, Alan
Kumpatla, Siva
Jacobs, John
Tomkins, Jeff
Cantrell, Roy
Main, Dorrie
author_facet Blenda, Anna
Scheffler, Jodi
Scheffler, Brian
Palmer, Michael
Lacape, Jean-Marc
Yu, John Z
Jesudurai, Christopher
Jung, Sook
Muthukumar, Sriram
Yellambalase, Preetham
Ficklin, Stephen
Staton, Margaret
Eshelman, Robert
Ulloa, Mauricio
Saha, Sukumar
Burr, Ben
Liu, Shaolin
Zhang, Tianzhen
Fang, Deqiu
Pepper, Alan
Kumpatla, Siva
Jacobs, John
Tomkins, Jeff
Cantrell, Roy
Main, Dorrie
author_sort Blenda, Anna
collection PubMed
description BACKGROUND: The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. CONCLUSION: The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.
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spelling pubmed-15390202006-08-11 CMD: a Cotton Microsatellite Database resource for Gossypium genomics Blenda, Anna Scheffler, Jodi Scheffler, Brian Palmer, Michael Lacape, Jean-Marc Yu, John Z Jesudurai, Christopher Jung, Sook Muthukumar, Sriram Yellambalase, Preetham Ficklin, Stephen Staton, Margaret Eshelman, Robert Ulloa, Mauricio Saha, Sukumar Burr, Ben Liu, Shaolin Zhang, Tianzhen Fang, Deqiu Pepper, Alan Kumpatla, Siva Jacobs, John Tomkins, Jeff Cantrell, Roy Main, Dorrie BMC Genomics Database BACKGROUND: The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. CONCLUSION: The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp. BioMed Central 2006-05-31 /pmc/articles/PMC1539020/ /pubmed/16737546 http://dx.doi.org/10.1186/1471-2164-7-132 Text en Copyright © 2006 Blenda et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Database
Blenda, Anna
Scheffler, Jodi
Scheffler, Brian
Palmer, Michael
Lacape, Jean-Marc
Yu, John Z
Jesudurai, Christopher
Jung, Sook
Muthukumar, Sriram
Yellambalase, Preetham
Ficklin, Stephen
Staton, Margaret
Eshelman, Robert
Ulloa, Mauricio
Saha, Sukumar
Burr, Ben
Liu, Shaolin
Zhang, Tianzhen
Fang, Deqiu
Pepper, Alan
Kumpatla, Siva
Jacobs, John
Tomkins, Jeff
Cantrell, Roy
Main, Dorrie
CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title_full CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title_fullStr CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title_full_unstemmed CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title_short CMD: a Cotton Microsatellite Database resource for Gossypium genomics
title_sort cmd: a cotton microsatellite database resource for gossypium genomics
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539020/
https://www.ncbi.nlm.nih.gov/pubmed/16737546
http://dx.doi.org/10.1186/1471-2164-7-132
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