Browse > Article
http://dx.doi.org/10.3745/KIPSTD.2005.12D.5.755

An XML-Based Analysis Tool for Gene Prediction Results  

Kim Jin-Hong (울산대학교 컴퓨터 정보통신공학부)
Byun Sang-Hee (울산대학교 컴퓨터 정보통신공학부)
Lee Myung-Joon (울산대학교 컴퓨터 정보통신공학부)
Park Yang-Su (울산대학교 컴퓨터 정보통신공학부)
Publication Information
The KIPS Transactions:PartD / v.12D, no.5, 2005 , pp. 755-764 More about this Journal
Abstract
Recently, as it is considered more important to identify the function of ail unknown genes in living things, many tools for gene prediction have been developed to identify genes in the DNA sequences. Unfortunately, most of those tools use their own schemes to represent their programs results, requiring researchers to make additional efforts to understand the result generated by them So, it is desirable to provide a standardized method of representing predicted gene information, which makes it possible to automatically produce the predicted results for a given set of gene data In this paper, we describe an effective U representation for various predicted gene information, and present an XML-based analysis tool for gene predication results based on this representation. The developed system helps users of gene prediction tools to conveniently analyze the predicted results and to automatically produce the statistical results of the prediction. To show the usefulness of the tool, we applied our programs to the results generated by GenScan and GeneID, which are widely used gene prediction systems.
Keywords
Gene Prediction; Gene Analysis; GenStructML; GenPredML; XML;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Burge C. and Karlin, S., 'Finding the genes in genomics DNA,' Current Opinion in Structural Biology, Vol.8, pp. 346-354, 1998   DOI   ScienceOn
2 Guigo, R., Agarwal, P., Abril, J.F., Burset, M. and Fickett, J.W., 'An Assessment of Gene Prediction Accuracy in Large DNA Sequences,' Genome Research Vol.10, No.10, pp. 1631-1642, 2000   DOI
3 Burge, C, 'Identification of genes in human genomic DNA,' PhD thesis, Stanford University, Stanford, CA., 1997
4 Burge, C. and Karlin, S., 'Prediction of complete gene structures in human genomic DNA,' J Mol BioI, Vol.266, pp.78-95, 1997   DOI   ScienceOn
5 Burset M, Guigo R, 'Evaluation of gene structure prediction programs,' Genomics, Vol.35, pp.353-367, 1996   DOI   ScienceOn
6 The Apache Software Foundation, Xerces : XML parsers in Java, Apache XML Project, WWW document (http:// xml.apache.org/), 2004
7 W3C, Document Object Model(DOM) Levell Specification, Ver. 1.0, WWW document (http://www.w3.org/TR/RECDOM-Level-1/), 1998
8 Ana, P., Pedro T., 'DECIDE - Gene Finding Evaluation Tool', WWW document (http://decide.inesc-id.pt/index.php), 2005
9 Rogic, S., Mackworth, AK., Ouellette, FB., 'Evalution of gene-finding programs on mammalian sequences,' Genome Research, Vol.11, No.5, pp.817-832, 2001   DOI   ScienceOn
10 Burset, M. and Guigo, R, 'Evaluation of gene structure prediction programs,' Genomics, Vol.35, pp.353-367, 1996   DOI   ScienceOn
11 Yergeau, F., Bray, T. and Paoli, J., Sperberg-McQueen CM, Maler E : Extensible Markup Language (XML) 1.0, 3rd Ed., W3C, 2004
12 Dennis, B., Ilene Karsch-Mizachi, David, L., James, O., Barbara R. and David, W., 'GenBank. Nucleic Acids Research,' Vol .28, No.1, pp.15-18, 2000   DOI
13 Dennis, B., Ilene Karsch-Mizachi, David, L., James, O., Barbara, R. and David, W., 'GenBank. Nucleic Acids Research,' Vol.32, No. 1, pp.23-26, 2004   DOI
14 DDBJ, EMBL and GenBank, The DDBJ/EMBL/GenBank Feature Table: Definition, Ver. 6.0, 2003
15 GFF, GFF (General Feature Format) Specifications Document, WWW document (http//www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml), 2004