CMD - Cotton Marker Database
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The Cotton Marker Database (CMD) is a curated and integrated web-based relational database providing centralized access to all publicly available cotton microsatellites and single nucleotide polymorphisms. In addition, CMD displays data for five of the microsatellite projects that have been screened against a standardized panel of core germplasm including 12 diverse genotypes. A suite of online 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 CMD cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs and SNPs, and CMap, a viewer for comparing cotton SSR maps. The collection of all publicly available cotton SSR and SNP markers into a centralized, readily accessible web-enabled database provides a more efficient utilization of molecular marker resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

Web and database hosting for the CMD is provided by Bioinformatics and Chemical Informatics (BCI) group at School of Computing, Clemson University.
Computational resources are provided by Clemson Computing and Information Technology (CCIT).
CMD logo and webpage design by Olga Reukova.

Referencing CMD:
Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J-M, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D. 2006. CMD: A Cotton Microsatellite Database Resource for Gossypium Genomics. BMC Genomics. 7:132

The CMD Development Team:

  Name   Role
    Principal Investigator
    Graduate Student, Database Development and Applications
    Undergraduate Student

The CMD Advisory Group:
  Name   Organization
    Cotton Incorporated
    Monsanto
    USDA-ARS, MS
    Dow AgroSciences
    CIRAD, France
    Stoneville Pedigree Seed-Monsanto
    TAMU
    USDA-ARS, MS
    USDA-ARS, MS
    USDA-ARS, MS
    TAMU
    USDA-ARS, CA
    USDA-ARS, TX
    Bayer CropScience
    UC Davis
    CottonDB
    USDA-ARS, TX
    UGA

 

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