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.
The RNA-Seq reads and ESTs were assembled by using the Mainlab RefTrans pipeline (manuscript in preparation – details of pipeline provided ahead of publication on request). The RefTran sequences were functionally characterized by pairwise comparison using the BLASTX algorithm against the Swiss-Prot and TrEMBL protein databases. Information on the top 25 matches with an expectation (E) value of ≤ 1E-06 were recorded and stored in CottonGen together with the RefTrans sequences. InterPro domains and Gene Ontology assignments were made using InterProScan at the EBI through Blast2GO. For more specific details on the materials and methods see the individual Gossypium species RefTrans page.