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

Overview

Journal Genome Res

Specialty Genetics

Date 2001 Sep 7

PMID 11544202

Citations 37

Authors

T Wiehe

S Gebauer-Jung

T Mitchell-Olds

R Guigo

Affiliations

Soon will be listed here.

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 depends little on species-specific properties such as codon usage or the nucleotide distribution. 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.

Citing Articles

Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis.

Xie J, Miao Y, Zhang X, Zhang G, Guo B, Luo G J Plant Res. 2023; 137(1):37-48.

PMID: 37917204 DOI: 10.1007/s10265-023-01502-3.

Integrated entropy-based approach for analyzing exons and introns in DNA sequences.

Li J, Zhang L, Li H, Ping Y, Xu Q, Wang R BMC Bioinformatics. 2019; 20(Suppl 8):283.

PMID: 31182012 PMC: 6557737. DOI: 10.1186/s12859-019-2772-y.

Whole-Genome Alignment and Comparative Annotation.

Armstrong J, Fiddes I, Diekhans M, Paten B Annu Rev Anim Biosci. 2018; 7:41-64.

PMID: 30379572 PMC: 6450745. DOI: 10.1146/annurev-animal-020518-115005.

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation.

Dunne M, Kelly S BMC Genomics. 2018; 19(1):307.

PMID: 29703150 PMC: 5923031. DOI: 10.1186/s12864-018-4704-z.

An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm.

Chowdhury B, Garai A, Garai G BMC Bioinformatics. 2017; 18(1):460.

PMID: 29065853 PMC: 5655831. DOI: 10.1186/s12859-017-1874-7.

References

Bafna V, Huson D . The conserved exon method for gene finding. Proc Int Conf Intell Syst Mol Biol. 2000; 8:3-12. View

Wiehe T, Guigo R, Miller W . Genome sequence comparisons: hurdles in the fast lane to functional genomics. Brief Bioinform. 2001; 1(4):381-8. DOI: 10.1093/bib/1.4.381. View

Gelfand M, Mironov A, Pevzner P . Gene recognition via spliced sequence alignment. Proc Natl Acad Sci U S A. 1996; 93(17):9061-6. PMC: 38595. DOI: 10.1073/pnas.93.17.9061. View

Claverie J . Computational methods for exon detection. Mol Biotechnol. 1998; 10(1):27-48. DOI: 10.1007/BF02745861. View

Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A . The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell. 2000; 12(3):381-91. PMC: 139838. DOI: 10.1105/tpc.12.3.381. View

Britten R . Rates of DNA sequence evolution differ between taxonomic groups. Science. 1986; 231(4744):1393-8. DOI: 10.1126/science.3082006. View

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

Burset M, Guigo R . Evaluation of gene structure prediction programs. Genomics. 1996; 34(3):353-67. DOI: 10.1006/geno.1996.0298. View

Blanc G, Barakat A, Guyot R, Cooke R, Delseny M . Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell. 2000; 12(7):1093-101. PMC: 149051. DOI: 10.1105/tpc.12.7.1093. View

10.

Vision T, Brown D, Tanksley S . The origins of genomic duplications in Arabidopsis. Science. 2000; 290(5499):2114-7. DOI: 10.1126/science.290.5499.2114. View

11.

Batzoglou S, Pachter L, Mesirov J, Berger B, Lander E . Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000; 10(7):950-8. PMC: 310911. DOI: 10.1101/gr.10.7.950. View

12.

Burge C, Karlin S . Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997; 268(1):78-94. DOI: 10.1006/jmbi.1997.0951. View

13.

Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, Fischer C . Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet. 2000; 25(2):235-8. DOI: 10.1038/76118. View

14.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

15.

Hardison R, Oeltjen J, Miller W . Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res. 1997; 7(10):959-66. DOI: 10.1101/gr.7.10.959. View

16.

Li W, Tanimura M, Sharp P . An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol. 1987; 25(4):330-42. DOI: 10.1007/BF02603118. View

17.

Sharp P, Averof M, LLOYD A, Matassi G, Peden J . DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci. 1995; 349(1329):241-7. DOI: 10.1098/rstb.1995.0108. View

18.

Novichkov P, Gelfand M, Mironov A . [Prediction of the exon-intron structure by comparing nucleotide sequences from various genomes]. Mol Biol (Mosk). 2000; 34(2):230-6. View

19.

Guigo R, Agarwal P, Abril J, Burset M, Fickett J . An assessment of gene prediction accuracy in large DNA sequences. Genome Res. 2000; 10(10):1631-42. PMC: 310940. DOI: 10.1101/gr.122800. View

20.

Delcher A, Kasif S, Fleischmann R, Peterson J, White O, Salzberg S . Alignment of whole genomes. Nucleic Acids Res. 1999; 27(11):2369-76. PMC: 148804. DOI: 10.1093/nar/27.11.2369. View