|Analysis Name||Gossypium unigene v1.0 |
|Source||Genbank Gossypium ESTs (September 16, 2012) |
|Date performed||2012-09-27 |
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.
| Processing Summary
| Number of ESTs available
| Number of ESTs available after filtering
| Average Length
| Number of Contigs(CAP3 Assembly, -p 90 )
| Average Length of Contigs
| Number of Singlets
| Number of Putative Unigenes
- Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
- 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.
- 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.
- Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, DÃ©jardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, KangasjÃ¤rvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, LeplÃ© JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, RouzÃ© P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). (2006) Science. Sep 15; 313(5793):1596-604
- 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.
Additional information about this analysis:
|Property Name||Value |
|Analysis Type||tripal_analysis_unigene |
|Analysis unigene name||Gossypium unigene v1.0 |
|Analysis unigene num contigs|| |
|Analysis unigene num reads|| |
|Analysis unigene avg length|| |
|Analysis unigene num clusters|| |
|Analysis unigene num singlets|| |
All Gossypium unigene v1.0 contigs were uploaded to the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main. The SBH (single-directional best hit) method was selected under the category "Assignment method". All other settings were defaults. Results were downloaded in the heir.tar.gz heirarchy file and uploaded to the website. Click the Downloads link on the sidebar for downloadable files. Analysis details can be found here.
InterPro domains and Gene Ontology assignments were made to Gossypium Unigene v1.0 contigs using InterProScan on a copmutational cluster at Washington State Univeristy by the Main bioinforamtics Lab. Click the Downloads link on the sidebar for downloadable files. Analysis details can be found here.
Homology was determined using the BLASTx algorithm for the Gossypium Contigs and Singlets vs. the Swiss-Prot, TrEMBL, TAIR Arabidopsis proteins, Prunus persica, Populus trichocarpa and Vitis vinifera proteins. Only matches with an E-value of =<1.0 e-6 r were recorded. Swiss-Prot is a curated protein database with a high level of annotation and a minimal level of redundancy, and TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of TrEMBL nucleotide sequence entries not yet integrated in Swiss-Prot. Homology of Gossypium in Excel spreadsheet can be downloaded from the Downloads page.
The Gossypium ESTs used for this assembly were downloaded on Sepermber 16, 2012
| EST Libraries
| Number of ESTs available
| # of Species
| # of Libraries
| # of Tissues
| # of Development Stages
View detailed chart of libraries.
| Gossypium arboreum
| Gossypium barbadense
|Gossypium herbaceum subsp. africanum
| Gossypium hirsutum
| Gossypium raimondii
The type and frequency of simple sequence repeats in Gossypium unigene v1.0 contigs was determined using the MainLabssr.pl program.For these searches, SSRs are defined as dinucleotides repeated at least 5 times, trinucleotides repeated at least 4 times, tetranucleotides repeated at least 3 times, or pentanucleotides repeated at least 3 times. The SSRs of Gossypium unigene v1.0 contigs are available to be downloaded from the Downloads link on the left sidebar.
|Number of Sequences
|Number of Sequences Having One Or More SSRs
|Percentage of Sequences Having One Or More SSRs
|Total Number of SSRs Found
|Number of Motifs
Frequency of Motif Type