Databases and tools for browsing genomes

被引:20
作者
Birney, E
Clamp, M
Hubbard, T
机构
[1] European Bioinformat Inst EMBL EBI, Hinxton CB10 1SA, Cambs, England
[2] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England
关键词
genome sequence; gene prediction; relational database; open source software; distributed annotation;
D O I
10.1146/annurev.genom.3.030502.101529
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
To maximize the value of genome sequences they need to be integrated with other types of biological data and with each other. The entire collection of data then needs to be made available in a way that is easy to view and mine for complex relationships. The recently determined vertebrate genome sequences of human and mouse are so large that building the infrastructure to manage these datasets is a major challenge. This article reviews the database systems and tools for analysis that have so far been developed to address this.
引用
收藏
页码:293 / 310
页数:20
相关论文
共 42 条
  • [1] ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
  • [2] InterPro - an integrated documentation resource for protein families, domains and functional sites
    Apweiler, R
    Attwood, TK
    Bairoch, A
    Bateman, A
    Birney, E
    Biswas, M
    Bucher, P
    Cerutti, L
    Corpet, F
    Croning, MDR
    Durbin, R
    Falquet, L
    Fleischmann, W
    Gouzy, J
    Hermjakob, H
    Hulo, N
    Jonassen, I
    Kahn, D
    Kanapin, A
    Karavidopoulou, Y
    Lopez, R
    Marx, B
    Mulder, NJ
    Oinn, TM
    Pagni, M
    Servant, F
    Sigrist, CJA
    Zdobnov, EM
    [J]. BIOINFORMATICS, 2000, 16 (12) : 1145 - 1150
  • [3] The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    Bairoch, A
    Apweiler, R
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 45 - 48
  • [4] Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
  • [5] The Molecular Biology Database Collection: 2002 update
    Baxevanis, AD
    [J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 1 - 12
  • [6] GenBank
    Benson, DA
    Karsch-Mizrachi, I
    Lipman, DJ
    Ostell, J
    Rapp, BA
    Wheeler, DL
    [J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 17 - 20
  • [7] BIRNEY E, 1997, ISMB, V5, P56
  • [8] Prediction of complete gene structures in human genomic DNA
    Burge, C
    Karlin, S
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1997, 268 (01) : 78 - 94
  • [9] SGD:: Saccharomyces Genome Database
    Cherry, JM
    Adler, C
    Ball, C
    Chervitz, SA
    Dwight, SS
    Hester, ET
    Jia, YK
    Juvik, G
    Roe, T
    Schroeder, M
    Weng, SA
    Botstein, D
    [J]. NUCLEIC ACIDS RESEARCH, 1998, 26 (01) : 73 - 79
  • [10] CONSORTIUM F, 2002, NUCLEIC ACIDS RES, V30, P106