Gossypium unigene v1.0

This is the first version of the Gossypium unigene. This build used ESTs downloaded from the genus Gossypium in the NCBI dbEST database.  The Gossypium ESTs included in this assembly were downloaded on September 16, 2012.

Not all of the Gossypium ESTs are of high quality. To filter, we crossmatched the public sequences against NCBI's UniVec database and used the BLAST sequence similarity algorithm to remove species-specific chloroplast, mitochondrial, tRNA, and rRNA sequences. To reduce redundancy and create longer transcripts we assembled these ESTs using the CAP3¹ program. The final assembly has been annotated by BLAST sequence similarity searching against Swiss-Prot², TrEMBL³, TAIR⁴ Arabidopsis proteins, Prunus persica⁵, Populus trichocarpa⁶ and Vitis vinifera⁷.

For more information on this project please contact the Cottongen development team.

References

1. Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
3. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Sneider M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research. 31:365-370.
4. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gate way to Arabidopsis biology, research materials and community. Nucleic Acids Research. 31(1):224-8.
5. http://services.appliedgenomics.org/projects/drupomics/
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7. French-Italian Public Consortium for Grapevine Genome Characterization.(2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. Sep 27; 449(7161):463-7.