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Vol. 11, Issue 9, 1574-1583, September 2001

METHODS
SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments

Thomas Wiehe,1,3 Steffi Gebauer-Jung,1 Thomas Mitchell-Olds,1 and Roderic Guigó2

1 Max Planck Institute for Chemical Ecology, Jena, Germany; 2 Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Barcelona, Spain

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.

3 Corresponding author.

11:1574-1583 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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