cDNA2Genome: A tool for mapping and annotating cDNAs

BMC Bioinformatics

Volumn 4, Issue , 2003, Pages

  del Val, Coral ^a   Glatting, Karl Heinz ^a   Suhai, Sandor ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; DNA;

ACCURACY; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; EXON; EXPRESSED SEQUENCE TAG; GENE IDENTIFICATION; GENE INSERTION; GENE MAPPING; GENE STRUCTURE; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; INTERNET; INTRON; MOLECULAR CLONING; MOUSE; NONHUMAN; PREDICTION; QUALITY CONTROL; RIBOSOMAL FRAMESHIFTING; SEQUENCE ANALYSIS; STOP CODON; BIOLOGY; CHROMOSOME MAP; COMPARATIVE STUDY; GENETICS; HUMAN GENOME; PHYSIOLOGY; PREDICTIVE VALUE; PROCEDURES; SEQUENCE ALIGNMENT; STANDARDS; TIME;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; DNA, COMPLEMENTARY; EXONS; GENOME, HUMAN; HUMANS; INTERNET; INTRONS; PREDICTIVE VALUE OF TESTS; SEQUENCE ALIGNMENT; SOFTWARE; SOFTWARE DESIGN; TIME FACTORS;

EID: 2942521203     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-39     Document Type: Article

References (19)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E and et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C and et al.: The sequence of the human genome. Science 2001, 291:1304-1351.
3. Stein L: Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2:493-503.
4. Sakaki Y, Hattori M, Toyoda A, Watanabe H, Yada T, Taylor T, Park HS, Totoki Y and Fujiyama A: [Determination of DNA sequence of the whole chromosome 21]. Tanpakushitsu Kakusan Koso 2000, 45:2520-2527.
5. Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Bocher M, Blocker H, Bauersachs S, Blum H, Lauber J, Dusterhoft A, Beyer A, Kohrer K, Strack N, Mewes HW, Ottenwalder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M and Poustka A: Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res 2001, 11:422-435.
6. Jenuth JP: The NCBI. Publicly available tools and resources on the Web. Methods Mol Biol 2000, 132:301-312.
7. Ernst P, Glatting KH and Suhai S: A task framework for the web interface W2H. Bioinformatics 2003, 19:278-282.
8. Senger M, Flores T, Glatting K, Ernst P, Hotz-Wagenblatt A and Suhai S: W2H: WWW interface to the GCG sequence analysis package. Bioinformatics 1998, 14:452-457.
9. Etzold T, Ulyanov A and Argos P: SRS: information retrieval system for molecular biology data banks. Methods Enzymol 1996, 266:114-128.
10. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
11. Zhang Z, Schwartz S, Wagner L and Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-214.
12. Burge C and Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
13. 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.
14. Guigo R, Knudsen S, Drake N and Smith T: Prediction of gene structure. J Mol Biol 1992, 226:141-157.
15. Florea L, Hartzell G, Zhang Z, Rubin GM and Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998, 8:967-974.
16. Birney E and Durbin R: Using GeneWise in the Drosophila annotation experiment. Genome Res 2000, 10:547-548.
17. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I and Clamp M: The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41.
18. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM and Haussler D: The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM and Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.