SGP-1: prediction and validation of homologous genes based on sequence alignments

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• dc.contributor.author Wiehe, Thomasca
• dc.contributor.author Gebauer-Jung, Steffica
• dc.contributor.author Mitchell-Olds, Thomasca
• dc.contributor.author Guigó Serra, Rodericca
• dc.date.accessioned 2012-05-21T09:44:52Z
• dc.date.available 2012-05-21T09:44:52Z
• dc.date.issued 2001ca
• dc.description.abstract Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of SGP-1 depends little on species-specific properties such as codon usage or the nucleotide distribution. SGP-1 may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.
• dc.format.mimetype application/pdfca
• dc.identifier.citation Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guigó R. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res. 2001;11(9):1574-83. DOI: 10.1101/gr.177401ca
• dc.identifier.doi http://dx.doi.org/10.1101/gr.177401
• dc.identifier.issn 1088-9051ca
• dc.identifier.uri http://hdl.handle.net/10230/16469
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press-CSHL Pressca
• dc.relation.ispartof Genome Research. 2001;11(9):1574-83
• dc.rights © 2001 Genome Research by Cold Spring Harbor Laboratory Press. Published version available at http://genome.cshlp.org. Aquest document està subjecte a Llicència Creative Commons (Attribution-NonCommercial 3.0 Unported License)ca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
• dc.subject.other Genòmica -- Informàtica
• dc.subject.other Factors de transcripció
• dc.title SGP-1: prediction and validation of homologous genes based on sequence alignmentsca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersion