DEVELOPMENT OF A COTTON MICROSATELLITE DATABASE (CMD)

Doreen Main and Jeffrey P. Tomkins, Clemson University

The Cotton Microsatellite Database or CMD ( www.cottonssr.org) was created to provide the cotton community with the maximum amount of information and scientific data on Simple Sequence R epeat (SSR) or microsatellite DNA markers. There are currently nine SSR marker projects listed in CMD, for which eight have data publicly available. Together these comprise 3,606 SSRs. Each project is accessible via the overall project page and link to the individual project pages. The individual project pages have been redesigned to provide information on project contributors, a summary project description (approved by project principal investigator), and publications linked to abstracts, and all available mapping, standard panel screening data, primer, sequence and motif data, which are also accessible as downloadable files. The SSR Server tool has been redesigned to implement primer design also. Users uploading sequences to identify SSRs are also provided with optimal primer pairs identified by the program “Primer3.” 

The FASTA/BLAST sequence similarity servers have been redesigned to make them easier to search, with more explicit instructions provided. The databases that can be searched include all the EST SSRs clone sequences in CMD and the Genomic SSR clone sequences in CMD. This allows users to identify novel SSR markers as they develop new data sets and helps prevent redundancy of effort for the community. A new standardized panel web page was created containing a list of project data available for viewing and downloading. Access to the BNL, JESPR and CIR standardized panel screened data in the new format was added to this, as well as a timetable for the addition of new panel data. CMap, the comparative mapping viewer, was implemented in CMD with data from 3 mapping projects involving SSRs. A new search by markers feature form was added, which allows users to search by marker name, chromosome, or cross. The results are returned in a table with columns for marker name, chromosome location, locus, and cross.

New individual markers pages have been created, which are linked from all references to marker name. The individual marker page contains the sequence type, clone sequence, primer sequences, motif sequence(s), and ORF sequence, highlighted where possible on the actual sequence. A right hand navigation bar links out to the individual project page, known homologs, publications, and Genbank records (where available). All 3606 marker sequences have been searched against the NCBI non redundant protein database using the BLASTX algorithm, and the results have been uploaded into the revamped database schema. We currently display the best homolog match (linked to Genbank protein record) and the associated information about the alignment. Of the 3606 markers, 1050 are homologous to existing proteins. All columns (marker name, match accession #, expectation value, percentage identity, alignment length, organism, and protein description/function) can be custom sorted for display. The search homology page allows users to search the protein matches by match organism keyword or protein description/function. The homology results retuned link out to all individual marker(s) information. A view SSRs page displays the marker name (linked out to detailed marker info), sequence type, repeat motif(s), and location of longest ORF in the sequence. A new search by markers feature has been added, allowing users to search by marker name, chromosome, or cross.

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