CottonGen presentations at Cotton Breeders 2017 Tour (9/15/17)

The 2017 Cotton Breeders Tour will be held in Aizona, September 24-27, 2017.

CottonGen for breeding will be presented by Todd Campbell and  Josh Udall on Sunday September 24th in the 3.15 PM session. The presentations will be made available in CottonGen presentations.

Project Information

CottonGen RefTrans combines peer-reviewed published RNA-Seq and EST data sets to create a Reference Transcriptome (RefTrans) for individual Gossypium species and provides putative gene function identified by homology to known proteins.  The transcriptome and associated annotation are available to download, search by name, keyword (functional description), or mapped location, and view on the genome through JBrowse.

-- G. raimondii CottonGen RefTrans V1 (31,990)

Human-Readable Name-- G. raimondii CottonGen RefTrans V1 (31,990)
Database Path/mainlab/web/temp/db/cottongen/g.raimondii_reftransV1
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G. hirsutum CottonGen RefTrans V1 (93,449)

Human-Readable Name-- G. hirsutum CottonGen RefTrans V1 (93,449)
Database Path/mainlab/web/temp/db/cottongen/g.hirsutum_reftransV1
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G. barbadense CottonGen RefTrans V1 (57,777)

Human-Readable Name-- G. barbadense CottonGen RefTrans V1 (57,777)
Database Path/mainlab/web/temp/db/cottongen/g.barbadense_reftransV1
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

-- G. arboreum CottonGen RefTrans V1 (30,964)

Human-Readable Name-- G. arboreum CottonGen RefTrans V1 (30,964)
Database Path/mainlab/web/temp/db/cottongen/g.arboreum_reftransV1
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseCottonGen Database
RegEx/^(\S+).*/
Link-out Typelink

New BLAST interface on CottonGen (8/5/17)

We have upgraded to the Tripal BLAST module.  This new BLAST interface replaces the old BLAST and batch BLAST tools.  The new BLAST  allows for result hyperlinks to the genome scaffolds in JBrowse and links to the feature details in CottonGen and on NCBI.  You can access the new BLAST tool through the "Tools" menu in the header, or use the link on the left hand menu of the Species pages.