@article{Wiehe01092001,
author = {Wiehe, Thomas and Gebauer-Jung, Steffi and Mitchell-Olds, Thomas and Guigó, Roderic}, 
title = {SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments},
volume = {11}, 
number = {9}, 
pages = {1574-1583}, 
year = {2001}, 
doi = {10.1101/gr.177401}, 
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.}, 
URL = {http://genome.cshlp.org/content/11/9/1574.abstract}, 
eprint = {http://genome.cshlp.org/content/11/9/1574.full.pdf+html}, 
journal = {Genome Research} 
}