Reference based annotation with GeneMapper

Genome Biology

Volumn 7, Issue 4, 2006, Pages

  Chatterji, Sourav ^a   Pachter, Lior ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ACCURACY; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENOME ANALYSIS; HUMAN; INTERMETHOD COMPARISON; MOUSE; NONHUMAN; PERFORMANCE; PREDICTION; QUALITY CONTROL; RAT; SENSITIVITY AND SPECIFICITY; ALGORITHM; ANIMAL; CHROMOSOME MAP; EVALUATION; GENOME; GENOMICS; METHODOLOGY; NUCLEIC ACID DATABASE;

ALGORITHMS; ANIMALS; CHROMOSOME MAPPING; DATABASES, NUCLEIC ACID; GENOME, HUMAN; GENOMICS; HUMANS; MICE; RATS; SOFTWARE;

EID: 33745051802     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2006-7-4-r29     Document Type: Article

References (39)

1. The Aceview genes. [http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/].
2. Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, et al.: An overview of Ensembl. Genome Res 2004, 14:925-928.
3. Drysdale R, Crosby M, Gelbart W, Campbell K, Emmert D, Matthews B, Russo S, Schroeder A, Smutniak F, Zhang P, et al.: FlyBase: genes and gene models. Nucleic Acids Res 2005. 33(Database):D390-D395.
4. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
5. Kulp D, Haussler D, Reese M, Eeckman F: A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol 1996, 4:134-142.
6. 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.
7. Flicek P, Keibler E, Hu P, Korf I, Brent M: Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 2003, 13:46-54.
8. Parra G, Agarwal P, Abril J, Wiehe T, Fickett J, Guigó R: Comparative gene prediction in human and mouse. Genome Res 2003, 13:108-117.
9. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin E: Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003, 299:1391-1394.
10. McAuliffe J, Pachter L, Jordan M: Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics 2004, 20:1850-1860.
11. Chatterji S, Pachter L: Multiple organism gene finding by collapsed gibbs sampling. In RECOMB '04: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology Volume 8. San Deigo, CA, USA. New York, NY: ACM Press; 2004:187-193. March 27-31 2004
12. Chatterji S, Pachter L: Large multiple organism gene finding by collapsed Gibbs sampling. J Comput Biol 2005, 12:599-608.
13. Siepel A, Haussler D: Computational identification of evolutionarily conserved exons. In RECOMB '04: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology Volume 8. San Deigo, CA, USA. New York, NY: ACM Press; 2004:177-186. March 27-31 2004
14. Gross SS, Brent MR: Using multiple alignments to improve gene prediction. In RECOMB '05: Proceedings of the Ninth Annual International Conference on Computational Molecular Biology Cambridge, MA, USA; 2005:374-388. May 14-16 2005
15. Kim N, Shin S, Lee S: ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Res 2005, 15:566-576.
16. Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.
17. Kent W: BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
18. Huang X: Fast comparison of a DNA sequence with a protein sequence database. Microb Comp Genomics 1996, 1:281-291.
19. Gelfand M, Mironov A, Pevzner P: Gene recognition via spliced sequence alignment. Proc Natl Acad Sci USA 1996, 93:9061-9066.
20. Birney E, Clamp M, Durbin R: GeneWise and Genomewise. Genome Res 2004, 14:988-995.
21. Yeh RF, Lim LP, Burge CB: Computational inference of homologous gene structures in the human genome. Genome Res 2001, 11:803-816.
22. Allen JE, Salzberg SL: JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 2005, 21:3596-3603.
23. Brejova B, Brown DG, Li M, Vinar T: ExonHunter: a comprehensive approach to gene finding. Bioinformatics 2005:i57-i65.
24. Meyer I, Durbin R: Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res 2004, 32:776-783.
25. GeneMapper Supplementary Webpage [http://bio.math.berkeley.edu/genemapper/suppl.html]
26. Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS: The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
27. The GENCODE Project: encyclopedia of genes and genes variants [http://genome.imim.es/gencode/]
28. Keibler E, Brent MR: Eval: a software package for analysis of genome annotations. BMC Bioinformatics 2003, 4:50.
29. Burset M, Guigo R: Evaluation of gene structure prediction programs. Genomics 1996, 34:353-367.
30. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al.: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
31. StrataSplice-A human splice site predictor [http://www.sanger.ac.uk/Software/analysis/stratasplice]
32. Dayhoff M, Schwartz R, Orcutt B: A model of evolutionary change in protein. In Atlas of Protein Sequences and Structure Volume 5. Washington DC: National Biomedical Research Foundation; 1978:345-352.
33. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919.
34. Durbin R, Eddy S, Krogh A, Mitchison G: Biological Sequence Analysis: Probablistic Models of Proteins and Nucleic Acids Cambridge: Cambridge University Press; 1998.
35. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
36. Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA: Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res 2000, 10:1304-1306.
37. Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L: Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res 2004, 14:661-664.
38. Boguski MS, Lowe TM, Tolstoshev CM: dbEST: database for 'expressed sequence tags'. Nat Genet 1993, 4:332-333.
39. Ashurst JL, Chen CK, Gilbert JGR, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S, et al.: The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res 2005, 33 (Database):D459-D465.