CottonGen Synteny Viewer
View synteny among Cotton genomes using the new Tripal Synteny Viewer
CottonGen Sequence Retrieval
Sequence Retrieval allows users to download nucleotide and protein sequences including chromosomes, scaffolds, genes, mRNAs, transcript coding sequences, protein, reftrans contigs and unigene contigs. For the sequences aligned to larger sequences, such as genes, mRNAs and transcript coding sequences, a numeric value specifying the number of upstream bases and downstream bases can be entered.
Primer3web version 4.0.0 allows users to pick PCR primers from a DNA sequence.
CottonGen Map Viewer
MapViewer is a graphical tool for viewing and comparing *Gossypium* spp. genetic maps. It includes dynamically scrollable maps, correspondence matrices, dot plots, links to details about map features, and exporting functionality. It was developed by the MainLab at Washington State University and is available for download for use in other Tripal databases.
CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the Whole Genomes and Chloroplast Genomes is available together with a JBrowse tutorial for more details about how to navigate and use JBrowse.
CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from *Gossypium* species. This can be done using nucleotide sequences or peptide sequences. BLAST functionality is similar to that on NCBI.
Data from: Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.)
To enrich available transcriptome data and identify genes potentially involved in fruit quality, RNA sequencing was performed on fruit tissue from two northern-adapted hybrid blueberry breeding populations.
CottonGen CottonCyc Pathways Database
The CottonGen CottonCyc Pathways Database supports searching and browsing the CottonCyc databases: * Cyc pathways for JGI v2.0 *G. raimondii* D5 genome assembly * Cyc pathways for CGP-BGI v1.0 *G. hirsutum* AD1 genome assembly
CottonGen Breeding Information Management System (BIMS)
BIMS, the Breeding Information Management System, is a secure and comprehensive online breeding management system developed for the generic Tripal Database Platform which allows breeders to store, manage, archive and analyze their private breeding program. Breeders can load data in templates provided as well as output from the Field Book App, an android app for collecting phenotype data. In addition to the private breeders BIMS, users without accounts can also view the publicly available breeding data. The fully developed version will allow users to: * Fully integrate their data with publicly available genomic, genetic and breeding data in the community database. * Utilize their integrated pedigree, phenotype and genotype data in performing genomic analysis and making breeding decisions. * Use open-source new genomics tool and breeding decision tools with seamless access to HPC.