WebScipio: An online tool for the determination of gene structures using protein sequences

被引：22
作者：
Odronitz F. [1 ]
Pillmann H. [1 ]
Keller O. [2 ]
Waack S. [2 ]
Kollmar M. [1 ]
机构：
[1] Max-Planck-Institut für Biophysikalische Chemie, Abteilung NMR-basierte Strukturbiologie, 37077 Göttingen
[2] Universität Göttingen, Institut für Informatik, 37083 Göttingen
来源：
BMC Genomics | / 9卷 / 1期
关键词：
Eukaryotic Genome; Protein Query; Common Marmoset; Simple Object Access Protocol; Index File;
D O I：
10.1186/1471-2164-9-422
中图分类号：
学科分类号：
摘要：
Background: Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. Results: WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. Conclusion: WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org. © 2008 Odronitz et al; licensee BioMed Central Ltd.
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共 25 条
[1]  
Dubchak I., Frazer K., Multi-species sequence comparison: The next frontier in genome annotation, Genome Biology, 4, 12, (2003)
[2]  
Bird C.P., Stranger B.E., Dermitzakis E.T., Functional variation and evolution of non-coding DNA, Curr Opin Genet Dev, 16, 6, pp. 559-564, (2006)
[3]  
Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., Kuehn M.S., Taylor C.M., Neph S., Koch C.M., Asthana S., Malhotra A., Adzhubei I., Greenbaum J.A., Andrews R.M., Flicek P., Boyle P.J., Cao H., Carter N.P., Clelland G.K., Davis S., Day N., Dhami P., Dillon S.C., Dorschner M.O., Fiegler H., Giresi P.G., Goldy J., Hawrylycz M., Haydock A., Humbert R., James K.D., Johnson B.E., Johnson E.M., Frum T.T., Rosenzw
[4]  
Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., Antonarakis S.E., Attwood J., Baertsch R., Bailey J., Barlow K., Beck S., Berry E., Birren B., Bloom T., Bork P., Botcherby M., Bray N., Brent M.R., Brown D.G., Brown S.D., Bult C., Burton J., Butler J., Campbell R.D., Carninci P., Cawley S., Chiaromonte F., Chinwalla A.T., Church D.M., Clamp M., Clee C., Collins F.S., Cook L.L., Copley R.R., Coulson A., Couronne O.
[5]  
Fischer D.F., Backendorf C., Identification of regulatory elements by gene family footprinting and in vivo analysis, Advances in Biochemical Engineering/Biotechnology, 104, pp. 37-64, (2007)
[6]  
Guigo R., Dermitzakis E.T., Agarwal P., Ponting C.P., Parra G., Reymond A., Abril J.F., Keibler E., Lyle R., Ucla C., Antonarakis S.E., Brent M.R., Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes, Proceedings of the National Academy of Sciences of the United States of America, 100, 3, pp. 1140-1145, (2003)
[7]  
Ner-Gaon H., Leviatan N., Rubin E., Fluhr R., Comparative cross-species alternative splicing in plants, Plant Physiology, 144, 3, pp. 1632-1641, (2007)
[8]  
Ureta-Vidal A., Ettwiller L., Birney E., Comparative genomics: Genome-wide analysis in metazoan eukaryotes, Nature Reviews, 4, 4, pp. 251-262, (2003)
[9]  
Kuhn R.M., Karolchik D., Zweig A.S., Trumbower H., Thomas D.J., Thakkapallayil A., Sugnet C.W., Stanke M., Smith K.E., Siepel A., Rosenbloom K.R., Rhead B., Raney B.J., Pohl A., Pedersen J.S., Hsu F., Hinrichs A.S., Harte R.A., Diekhans M., Clawson H., Bejerano G., Barber G.P., Baertsch R., Haussler D., Kent W.J., The UCSC genome browser database: Update 2007, Nucleic Acids Research, (2007)
[10]  
Elnitski L.L., Shah P., Moreland R.T., Umayam L., Wolfsberg T.G., Baxevanis A.D., The ENCODEdb portal: Simplified access to ENCODE Consortium data, Genome Research, 17, 6, pp. 954-959, (2007)
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