Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Tóm tắt
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Từ khóa
Tài liệu tham khảo
Brent MR: Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res. 2005, 15: 1777-1786. 10.1101/gr.3866105.
Zhang MQ: Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet. 2002, 3: 698-709. 10.1038/nrg890.
Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997, 268: 78-94. 10.1006/jmbi.1997.0951.
Majoros WH, Pertea M, Salzberg SL: TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004, 20: 2878-2879. 10.1093/bioinformatics/bth315.
Salamov AA, Solovyev VV: Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000, 10: 516-522. 10.1101/gr.10.4.516.
Lukashin AV, Borodovsky M: GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 1998, 26: 1107-1115. 10.1093/nar/26.4.1107.
Pavy N, Rombauts S, Dehais P, Mathe C, Ramana DV, Leroy P, Rouze P: Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics. 1999, 15: 887-899. 10.1093/bioinformatics/15.11.887.
Burset M, Guigo R: Evaluation of gene structure prediction programs. Genomics. 1996, 34: 353-367. 10.1006/geno.1996.0298.
Guigo R, Agarwal P, Abril JF, Burset M, Fickett JW: An assessment of gene prediction accuracy in large DNA sequences. Genome Res. 2000, 10: 1631-1642. 10.1101/gr.122800.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006, S21-S31. Suppl 1
Mott R: EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci. 1997, 13: 477-478.
Huang X, Adams MD, Zhou H, Kerlavage AR: A tool for analyzing and annotating genomic sequences. Genomics. 1997, 46: 37-45. 10.1006/geno.1997.4984.
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998, 8: 967-974.
Usuka J, Zhu W, Brendel V: Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics. 2000, 16: 203-211. 10.1093/bioinformatics/16.3.203.
Kent WJ: BLAT: the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664. 10.1101/gr.229202. Article published online before March 2002.
Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005, 21: 1859-1875. 10.1093/bioinformatics/bti310.
Slater GS, Birney E: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005, 6: 31-10.1186/1471-2105-6-31.
Birney E, Clamp M, Durbin R: GeneWise and Genomewise. Genome Res. 2004, 14: 988-995. 10.1101/gr.1865504.
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, et al: An overview of Ensembl. Genome Res. 2004, 14: 925-928. 10.1101/gr.1860604.
Korf I, Flicek P, Duan D, Brent MR: Integrating genomic homology into gene structure prediction. Bioinformatics. 2001, S140-S148. Suppl 1
Wei C, Brent MR: Using ESTs to improve the accuracy of de novo gene prediction. BMC Bioinformatics. 2006, 7: 327-10.1186/1471-2105-7-327.
Gross SS, Brent MR: Using multiple alignments to improve gene prediction. J Comput Biol. 2006, 13: 379-393. 10.1089/cmb.2006.13.379.
Stanke M, Schoffmann O, Morgenstern B, Waack S: Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006, 7: 62-10.1186/1471-2105-7-62.
Kulp D, Haussler D, Reese MG, Eeckman FH: Integrating database homology in a probabilistic gene structure model. Pac Symp Biocomput. 1997, 232-244.
Brejova B, Brown DG, Li M, Vinar T: ExonHunter: a comprehensive approach to gene finding. Bioinformatics. 2005, i57-i65. 10.1093/bioinformatics/bti1040. Suppl 1
Alexandersson M, Cawley S, Pachter L: SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 2003, 13: 496-502. 10.1101/gr.424203.
Majoros WH, Pertea M, Salzberg SL: Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics. 2005, 21: 1782-1788. 10.1093/bioinformatics/bti297.
Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD: Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol. 2005, 3: 7-10.1186/1741-7007-3-7.
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002, 3: RESEARCH0083-10.1186/gb-2002-3-12-research0083.
Loveland J: VEGA, the genome browser with a difference. Brief Bioinform. 2005, 6: 189-193. 10.1093/bib/6.2.189.
Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME: Apollo: a sequence annotation editor. Genome Biol. 2002, 3: RESEARCH0082-10.1186/gb-2002-3-12-research0082.
Berriman M, Rutherford K: Viewing and annotating sequence data with Artemis. Brief Bioinform. 2003, 4: 124-132. 10.1093/bib/4.2.124.
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O: Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003, 31: 5654-5666. 10.1093/nar/gkg770.
Allen JE, Pertea M, Salzberg SL: Computational gene prediction using multiple sources of evidence. Genome Res. 2004, 14: 142-148. 10.1101/gr.1562804.
Allen JE, Salzberg SL: JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics. 2005, 21: 3596-3603. 10.1093/bioinformatics/bti609.
Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM: Creating a honey bee consensus gene set. Genome Biol. 2007, 8: R13-10.1186/gb-2007-8-1-r13.
Djebali S, Delaplace F, Crollius HR: Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biol. 2006, S7.1-S7.10. Suppl 1
Pertea M: Gene finding in eukaryotes. PhD thesis. 2001, Johns Hopkins University, Baltimore, MA, USA
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, et al: Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007, 316: 1718-1723. 10.1126/science.1138878.
Haas BJ, Berriman M, Hirai H, Cerqueira GG, Loverde PT, El-Sayed NM: Schistosoma mansoni genome: closing in on a final gene set. Exp Parasitol. 2007, 117: 225-228. 10.1016/j.exppara.2007.06.005.
EVidenceModeler (EVM). [http://evidencemodeler.sourceforge.net]
Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL: Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 2002, 3: RESEARCH0029-10.1186/gb-2002-3-6-research0029.
Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y, Gaasterland T: Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res. 2003, 13: 1290-1300. 10.1101/gr.1017303.
Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA: Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol. 2006, 60: 69-85. 10.1007/s11103-005-2564-9.
Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T: Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res. 2006, 34: 3917-3928. 10.1093/nar/gkl507.
ENCODE Project Consotrium: The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004, 306: 636-640. 10.1126/science.1105136.
Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R: GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006, S4.1-S4.9. Suppl 1
Gene Structure Annotation and Analysis Using PASA. [http://pasa.sourceforge.net]
RepeatMasker Open-3.0. [http://www.repeatmasker.org]
Ouyang S, Buell CR: The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 2004, D360-D363. 10.1093/nar/gkh099. 32 Database
DFCI - Gene Indices. [http://compbio.dfci.harvard.edu/tgi/tgipage.html]
Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR: Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics. 2006, 7: 327-10.1186/1471-2164-7-327.
EGASP Project FTP Site. [ftp://genome.imim.es/pub/projects/gencode/data/egasp05/]
The JIGSAW Home Page. [http://www.cbcb.umd.edu/software/jigsaw/]
SourceForge.net: GLEAN. [http://sourceforge.net/projects/glean-gene]