Gene finding in novel genomes
Tóm tắt
Từ khóa
Tài liệu tham khảo
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
Webb CT, Shabalina SA, Ogurtsov AY, Kondrashov AS: Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res 2002, 30: 1233–1239. 10.1093/nar/30.5.1233
Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE: Genome annotation assessment in Drosophila melanogaster. Genome Res 2000, 10: 483–501. 10.1101/gr.10.4.483
Riboldi Tunnicliffe G, Gloeckner G, Elgar GS, Brenner S, Rosenthal A: Comparative analysis of the PCOLCE region in Fugu rubripes using a new automated annotation tool. Mamm Genome 2000, 11: 213–219. 10.1007/s003350010039
Kraemer E, Wang J, Guo J, Hopkins S, Arnold J: An analysis of gene-finding programs for Neurospora crassa. Bioinformatics 2001, 17: 901–912. 10.1093/bioinformatics/17.10.901
Boeddrich A, Burgtorf C, Francis F, Hennig S, Panopoulou G, Steffens C, Borzym K, Lehrach H: Sequence analysis of an amphioxus cosmid containing a gene homologous to members of the aldo-keto reductase gene superfamily. Gene 1999, 16: 207–214. 10.1016/S0378-1119(99)00079-7
Akashi H: Gene expression and molecular evolution. Curr Opin Genet Dev 2001, 11: 660–666. 10.1016/S0959-437X(00)00250-1
Lim LP, Burge CB: A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A 2001, 98: 11193–11198. 10.1073/pnas.201407298
Solovyev V, Salamov A: The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc Int Conf Intell Syst Mol Biol 1997, 5: 294–302.
Kulp D, Haussler D, Reese MG, Eeckman FH: A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol 1996, 4: 134–142.
Krogh A: Two methods for improving performance of an HMM and their application for gene finding. Proc Int Conf Intell Syst Mol Biol 1997, 5: 179–186.
Cawley SE, Wirth AI, Speed TP: Phat – a gene finding program for Plasmodium falciparum. Mol Biochem Parasitol 2001, 118: 167–174. 10.1016/S0166-6851(01)00363-2
Genefinder (Green P.)[http://ftp.genome.washington.edu/cgi-bin/genefinder_req.pl]
Stanke M, Waack S: Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19(Suppl 2):II215-II225.
Majoros WH, Pertea M, Antonescu C, Salzberg SL: GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res 2003, 31: 3601–3604. 10.1093/nar/gkg527
Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K: RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res 2002, 30: 98–102. 10.1093/nar/30.1.98
Pictogram (Burge C)[http://genes.mit.edu/pictogram.html]
The Institute for Genomic Research[http://www.tigr.org]
Ensembl Genome Browser[http://www.ensembl.org]
SRS7 at the Sanger Institute[http://srs.sanger.ac.uk]
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403–410. 10.1006/jmbi.1990.9999
WU-BLAST (Gish W)[http://blast.wustl.edu]
Bioperl, Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12: 1611–1618. 10.1101/gr.361602
RepeatMasker (Smit, AFA, Green P.)[http://repeatmasker.genome.washington.edu]