Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus

Bioinformatics

Volumn 20, Issue 7, 2004, Pages 1157-1169

  Brendel, Volker ^a,b   Xing, Liqun ^a,c   Zhu, Wei ^a,d  

^a IOWA STATE UNIVERSITY   (United States)

^b Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

^c BASF CORPORATION   (United States)

^d NEWLINK GENETICS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; RNA;

ACCURACY; ARABIDOPSIS; ARTICLE; BASE MISPAIRING; CAENORHABDITIS ELEGANS; CEREAL; COMPUTER PROGRAM; CONSENSUS SEQUENCE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE DELETION; GENE DUPLICATION; GENE INSERTION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC ANALYSIS; HUMAN; MATHEMATICAL COMPUTING; MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PREDICTION; PRIORITY JOURNAL; RICE; RNA SPLICING; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 2442690356     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth058     Document Type: Article

References (44)

1. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Blanc,G., Hokamp,K. and Wolfe,K.H. (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res., 13, 137-144.
3. Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) dbEST-database for 'expressed sequence tags'. Nat. Genet., 4, 332-333.
4. Bouck,J., Yu,W., Gibbs,R. and Worley,K. (1999) Comparison of gene indexing databases. Trends Genet., 15, 159-162.
5. Brendel,V. and Kleffe,J. (1998) Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucleic Acids Res., 26, 4748-4757.
6. Brett,D., Pospisil,H., Valcarcel,J., Reich,J. and Bork,P. (2002) Alternative splicing and genome complexity. Nat. Genet., 30, 29-30.
7. Brunak,S., Engelbrecht,J. and Knudsen,S. (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol., 220, 49-65.
8. Deutsch,M. and Long,M. (1999) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res., 27, 3219-3228.
9. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
10. Gaut,B.S. (2001) Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res., 11, 55-66.
11. Gelfand,M.S., Mironov,A.A. and Pevzner,P.A. (1996) Gene recognition via spliced sequence alignment. Proc. Natl Acad. Sci., USA, 93, 9061-9066.
12. Gusfield,D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York, pp. 152-155.
13. Haas,B.J., Delcher,A.L., Mount,S.M., Wortman,J.R., Smith,R.K.,Jr, Hannick,L.I., Maiti,R., Ronning,C.M., Rusch,D.B., Town,C.D., Salzberg,S.L. and White,O. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res., 31, 5654-5666.
14. Haas,B.J., Volfovsky,N., Town,C.D., Troukhar,M., Alexandrov,N., Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 3, research 0029.1-0029.12.
15. Hebsgaard,S.M., Korning,P.G., Tolstrup,N., Engelbrecht,J., Rouzé,P. and Brunak,S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res., 24, 3439-3452.
16. Huang,X., Adams,M.D., Zhou,H. and Kerlavage,A.R. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
17. Kalyanaraman,A., Aluru,S., Kothari,S. and Brendel,V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Res., 31, 2963-2974.
18. Kan,Z., Rouchka,E.C., Gish,W.R. and States,D.J. (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11, 889-900.
19. Kass,R.E. and Raftery,A.E. (1995) Bayes Factors. J. Am. Stat. Assoc., 90, 377-395.
20. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
21. Liang,F., Holt,I., Pertea,G., Karamycheva,S., Salzberg,S. and Quackenbush,J. (2000) An optimized protocol for analysis of EST sequences. Nucleic Acid Res., 28, 3657-3665.
22. Manber,U. and Myers,G. (1993) Suffix arrays: a new method for on-line string searches. SIAM J. Comput., 22, 935-948.
23. Mathé,C., Sagot,M.F., Schiex,T. and Rouzé,P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30, 4103-4117.
24. Mironov,A.A., Fickett,J.W. and Gelfand,M.S. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288-1293.
25. Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nat. Genet., 30, 13-19.
26. Mott,R. (1997) EST-GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
27. Murakami,K. and Takagi,T. (1998) Gene recognition by combination of several gene-finding programs. Bioinformatics, 14, 665-675.
28. Ogasawara,J. and Morishita,S. (2002) Fast and sensitive algorithm for aligning ESTs to human genome. In Proceedings of the First IEEE Computer Society Bioinformatics Conference. Stanford, California, pp. 43-53.
29. Pavy,N., Rombauts,S., Déhais,P., Mathé,C., Ramana,D.V., Leroy,P. and Rouzé,P. (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
30. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci., USA, 85, 2444-2448.
31. Pertea,G., Huang,X., Liang,F., Antonescu,V., Sultana,R., Karamycheva,S., Lee,Y., White,J., Cheung,F., Parvizi,B., Tsai,J. and Quackenbush,J. (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19, 651-652.
32. Pertea,M., Lin,X. and Salzberg,S.L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res., 29, 1185-1190.
33. Rogic,S., Mackworth,A.K. and Ouellette,F.B. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
34. Sakharkar,M., Long,M., Tan,T.W. and de Souza,S.J. (2000) ExInt: an exon/intron database. Nucleic Acids Res., 28, 191-192.
35. Salzberg,S.L. (1997) A method for identifying splicing sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci., 13, 365-376.
36. Schlueter,S.D., Dong,Q. and Brendel,V. (2003) GeneSeqer PlantGDB - gene structure prediction in plant genomes. Nucleic Acids Res., 31, 3597-3600.
37. Sharp,P.M. and Matassi,G. (1994) Codon usage and genome evolution. Curr. Opin. Genet. Dev., 4, 851-860.
38. Snyder,E.E. and Stormo,G.D. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol., 248, 1-18.
39. Usuka,J. and Brendel,V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.
40. Usuka,J., Zhu,W. and Brendel,V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics, 16, 203-211.
41. Wheelan,S.J., Church,D.M. and Ostell,J.M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res., 11, 1952-1957.
42. White,O., Soderlund,C., Shanmugan,P. and Fields,C. (1992) Information contents and dinucleotide composition of plant intron sequences vary with evolutionary origin. Plant Mol. Biol., 19, 1057-1064.
43. Zhu,W. and Brendel,V. (2003) Identification, characterization, and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Res., 31, 4561-4572.
44. Zhu,W., Schlueter,S.D. and Brendel,V. (2003) Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiol., 132, 469-484.