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Fiber Evolution

Introgression Populations
Homoeolog-specific Profiling
Genetic Networks & Phenotype
Effects of Selection
Sequence Capture

Genetic and Physical mapping resources
Comparative BAC Sequencing
Genome Sequence Resources
EST D-genome map
EST Resources

Web Database
Education and Outreach
Significance for cotton industry
Cotton Literature
Cotton Links
Wendel Lab
PGML (Paterson Lab)
Udall Lab

Lists & protocols
How to
CEGC Site Search

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Further Information

This project is generating a diverse set of data including EST sequences/ unigene sets, BAC sequences/ physical maps and expression profiles. We have implemented a number of search and visualization tools to accommodate these data types. Tools range from GMOD’s CMap and GBrowse, for genetic map and genomic views, to implementations of NCBI’s Web BLAST and the Stanford Microarray Database (SMD), for cotton sequence alignment and gene expression data. Also, we have developed search tools for our cotton array probes and genetic markers. These tools are illustrated and described in the following figures and captions.

The NCBI wwwBLAST tool has been implemented to provide users with the capability of BLASTing their sequences against our Cotton assemblies. It can be reached from the "EST resources" page.

The GMOD CMap tool has been implemented at the Plant Genome Mapping Lab to provide comparative views of Gossypium genetic map data. It can be reached from the “Genetic and Physical mapping resources” page or directly at

Our EST assembly search tool allows users to list contigs and select assembly views for alignment details or link to our implementation of the GMOD tool, GBrowse for views of our Gossypium assemblies/contigs in the Arabidopsis genomic context. We have implemented a contig viewer, developed in the Udall lab, for detailed contig assembly views.

Search tools for microarray probes, genetically mapped objects and physical mapping data are shown in the following figure. The arrayed and mapped objects portals display search results as lists of links to collaborator and external database resources. The arrayed objects portal can be reached via our Microarray component and the mapped objects portal via our "How to" page or directly. The physical mapping database is maintained by the Plant Genome Mapping Lab to facilitate searches of BAC hybridization and developing physical map related data.

Sample interfaces from our implementation of the Stanford Microarray Database are shown below. It can be reached from the “Microarray” page.

We welcome your comments and suggestions.