Databases and tools for browsing genomes

Annual Review of Genomics and Human Genetics

Volumn 3, Issue , 2002, Pages 293-310

  Birney, Ewan ^a   Clamp, Michele ^a   Hubbard, Tim ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Distributed annotation; Gene prediction; Genome sequence; Open source software; Relational database

Indexed keywords

BIOINFORMATICS; DATA BASE; GENE SEQUENCE; GENOME; HUMAN; HUMAN GENOME; INFORMATION SYSTEM; MOUSE; NONHUMAN; REVIEW; VERTEBRATE;

ANIMALS; DATABASES; GENETICS; GENOME; HUMANS; INTERNET; SOFTWARE;

VERTEBRATA;

EID: 0036403719     PISSN: 15278204     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genom.3.030502.101529     Document Type: Review

References (42)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Med. Biol. 215:403-10
2. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, et al. 2000. Inter-Pro - An integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:1145-50
3. Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:45-48
4. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, et al. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-80
5. Baxevanis AD. 2002. The Molecular Biology Database Collection: 2002 Update. Nucleic Acids Res. 30:1-12
6. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. 2002. GenBank. Nucleic Acids Res. 30:17-20
7. Birney E, Durbin R. 1997. Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. ISMB 5:56-64
8. Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94
9. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, et al. 1998. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26:73-79
10. Consortium F. 2002. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 30:106-8
11. Consortium IHGS. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
12. Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, et al. 2001. The DNA sequence and comparative analysis of human chromosome 20. Nature 414:865-71
13. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. 2001. The distributed annotation system. BMC Bioinform. 2:7
14. Durbin D, Thierry-Mieg J. 1991. A C. Elegans Database. http://www.sanger.ac.uk/Software/Acedb/
15. Eeckman FH, Durbin R. 1995. ACeDB and macace. Methods Cell Biol. 48:583-605
16. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8:967-74
17. Gelfand MS, Mironov AA, Pevzner PA. 1996. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. USA 93:9061-66
18. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, et al. 2002. The Ensembl Genome Database Project. Nucleic Acids Res. 30:38-41
19. Hubbard T, Birney E. 2000. Open annotation offers a democratic solution to genome sequencing. Nature 403:825
20. Kanehisa M, Goto S, Kawashima S, Nakaya A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:42-46
21. Kelley S. 2000. Getting started with Acedb. Brief Bioinform. 1:131-37
22. Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, et al. 2002. The Celera Discovery System. Nucleic Acids Res. 30:129-36
23. Korf I, Flicek P, Duan D, Brent MR. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17:S140-48
24. Krogh A. 2000. Using database matches with HMMGene for automated gene detection in Drosophila. Genome Res. 10:523-28
25. Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E. 2001. Progress in sequencing the mouse genome. Genesis 31:137-41
26. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. 2002. SCOP database in 2002: Refinements accommodate structural genomics. Nucleic Acids Res. 30:264-67
27. Mott R. 1997. EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci. 13:477-78
28. Mural RJ, Parang M, Shah M, Snoddy J, Uberbacher EC. 1999. The Genome Channel: A browser to a uniform first-pass annotation of genomic DNA. Trends Genet. 15:38-39
29. Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: A fast search method for large DNA databases. Genome Res. 11:1725-29
30. Pocock MR, Down T, Hubbard TJP. 2000. BioJava: Open source components for bioinformatics. SIGBIO Newsl. 20:10-12
31. Pruitt KD, Maglott DR. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29:137-40
32. Reese MG, Kulp D, Tammana H, Haussler D. 2000. Genie - Gene finding in Drosophila melanogaster. Genome Res. 10:529-38
33. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. 2000. Artemis: Sequence visualization and annotation. Bioinformatics 16:944-45
34. Smit AF. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9:657-63
35. Solovyev VV, Salamov AA, Lawrence CB. 1995. Identification of human gene structure using linear discriminant functions and dynamic programming. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3:367-75
36. Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J. 2001. WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29:82-86
37. Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, et al. 2002. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 30:21-26
38. Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, et al. 2002. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res. 30:27-30
39. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. 2001. The sequence of the human genome. Science 291:1304-51
40. Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, et al. 2002. The Protein Data Bank: Unifying the archive. Nucleic Acids Res. 30:245-48
41. Xu Y, Uberbacher EC. 1997. Automated gene identification in large-scale genomic sequences. J. Comput. Biol. 4:325-38
42. Yeh RF, Lim LP, Burge CB. 2001. Computational inference of homologous gene structures in the human genome. Genome Res. 11:803-16