The SNP Consortium website: past, present and future

被引:93
作者
Thorisson, GA [1 ]
Stein, LD [1 ]
机构
[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
关键词
D O I
10.1093/nar/gkg052
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or single nucleotide polymorphism (SNP) keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the data coordinating center (DCC) website (http://snp.cshl.org) are open source.
引用
收藏
页码:124 / 127
页数:4
相关论文
共 14 条
[1]   The Distributed Annotation System [J].
Dowell, Robin D. ;
Jokerst, Rodney M. ;
Day, Allen ;
Eddy, Sean R. ;
Stein, Lincoln .
BMC BIOINFORMATICS, 2001, 2 (1)
[2]   The structure of haplotype blocks in the human genome [J].
Gabriel, SB ;
Schaffner, SF ;
Nguyen, H ;
Moore, JM ;
Roy, J ;
Blumenstiel, B ;
Higgins, J ;
DeFelice, M ;
Lochner, A ;
Faggart, M ;
Liu-Cordero, SN ;
Rotimi, C ;
Adeyemo, A ;
Cooper, R ;
Ward, R ;
Lander, ES ;
Daly, MJ ;
Altshuler, D .
SCIENCE, 2002, 296 (5576) :2225-2229
[3]   The Ensembl genome database project [J].
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 ;
Clamp, M .
NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :38-41
[4]   The human genome browser at UCSC [J].
Kent, WJ ;
Sugnet, CW ;
Furey, TS ;
Roskin, KM ;
Pringle, TH ;
Zahler, AM ;
Haussler, D .
GENOME RESEARCH, 2002, 12 (06) :996-1006
[5]   Assembly of the working draft of the human genome with GigAssembler [J].
Kent, WJ ;
Haussler, D .
GENOME RESEARCH, 2001, 11 (09) :1541-1548
[6]  
MATISE TC, UNPUB NATURE
[7]   RefSeq and LocusLink: NCBI gene-centered resources [J].
Pruitt, KD ;
Maglott, DR .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :137-140
[8]   A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms [J].
Sachidanandam, R ;
Weissman, D ;
Schmidt, SC ;
Kakol, JM ;
Stein, LD ;
Marth, G ;
Sherry, S ;
Mullikin, JC ;
Mortimore, BJ ;
Willey, DL ;
Hunt, SE ;
Cole, CG ;
Coggill, PC ;
Rice, CM ;
Ning, ZM ;
Rogers, J ;
Bentley, DR ;
Kwok, PY ;
Mardis, ER ;
Yeh, RT ;
Schultz, B ;
Cook, L ;
Davenport, R ;
Dante, M ;
Fulton, L ;
Hillier, L ;
Waterston, RH ;
McPherson, JD ;
Gilman, B ;
Schaffner, S ;
Van Etten, WJ ;
Reich, D ;
Higgins, J ;
Daly, MJ ;
Blumenstiel, B ;
Baldwin, J ;
Stange-Thomann, NS ;
Zody, MC ;
Linton, L ;
Lander, ES ;
Altshuler, D .
NATURE, 2001, 409 (6822) :928-933
[9]   dbSNP: the NCBI database of genetic variation [J].
Sherry, ST ;
Ward, MH ;
Kholodov, M ;
Baker, J ;
Phan, L ;
Smigielski, EM ;
Sirotkin, K .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :308-311
[10]   The bioperl toolkit:: Perl modules for the life sciences [J].
Stajich, JE ;
Block, D ;
Boulez, K ;
Brenner, SE ;
Chervitz, SA ;
Dagdigian, C ;
Fuellen, G ;
Gilbert, JGR ;
Korf, I ;
Lapp, H ;
Lehväslaiho, H ;
Matsalla, C ;
Mungall, CJ ;
Osborne, BI ;
Pocock, MR ;
Schattner, P ;
Senger, M ;
Stein, LD ;
Stupka, E ;
Wilkinson, MD ;
Birney, E .
GENOME RESEARCH, 2002, 12 (10) :1611-1618