An interactive bovine in silico SNP database (IBISS)

被引：52

作者：

Hawken, RJ ^{[1
]}

Barris, WC ^{[1
]}

McWilliam, SM ^{[1
]}

Dalrymple, BP ^{[1
]}

机构：

[1] CSIRO, Livestock Ind, St Lucia, Qld, Australia

来源：

MAMMALIAN GENOME | 2004年 / 15卷 / 10期

关键词：

D O I：

10.1007/s00335-004-2382-4

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：

An interactive bovine in silico SNP (IBISS) database has been created through the clustering and aligning of bovine EST and mRNA sequences. Approximately 324,000 EST and mRNA sequences were clustered to produce 29,965 clusters (producing 48,679 consensus sequences) and 48,565 singletons. A SNP screening regime was placed on variations detected in the multiple sequence alignment files to determine which SNPs are more likely to be real rather than sequencing errors. A small subset of predicted SNPs was validated on a diverse set of bovine DNA samples using PCR amplification and sequencing. Fifty percent of the predicted SNPs in the "putative >1" category were polymorphic in the population sampled. The MISS database represents more than just a SNP database; it is also a genomic database containing uniformly annotated predicted gene mRNA and protein sequences, gene structure, and genomic organization information.

引用

页码：819 / 827

页数：9

共 37 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] An ordered comparative map of the cattle and human genomes [J].

Band, MR ;

Larson, JH ;

Rebeiz, M ;

Green, CA ;

Heyen, DW ;

Donovan, J ;

Windish, R ;

Steining, C ;

Mahyuddin, P ;

Womack, JE ;

Lewin, HA .

GENOME RESEARCH, 2000, 10 (09) :1359-1368

[3] A medium-density genetic linkage map of the bovine genome [J].

Barendse, W ;

Vaiman, D ;

Kemp, SJ ;

Sugimoto, Y ;

Armitage, SM ;

Williams, JL ;

Sun, HS ;

Eggen, A ;

Agaba, M ;

Aleyasin, SA ;

Band, M ;

Bishop, MD ;

Buitkamp, J ;

Byrne, K ;

Collins, F ;

Cooper, L ;

Coppettiers, W ;

Denys, B ;

Drinkwater, RD ;

Easterday, K ;

Elduque, C ;

Ennis, S ;

Erhardt, G ;

Ferretti, L ;

Flavin, N ;

Gao, Q ;

Georges, M ;

Gurung, R ;

Harlizius, B ;

Hawkins, G ;

Hetzel, J ;

Hirano, T ;

Hulme, D ;

Jorgensen, C ;

Kessler, M ;

Kirkpatrick, BW ;

Konfortov, B ;

Kostia, S ;

Kuhn, C ;

Lenstra, JA ;

Leveziel, H ;

Lewin, HA ;

Leyhe, B ;

Lil, L ;

Burriel, IM ;

McGraw, RA ;

Miller, JR ;

Moody, DE ;

Moore, SS ;

Nakane, S .

MAMMALIAN GENOME, 1997, 8 (01) :21-28

[4] Reliable identification of large numbers of candidate SNPs from public EST data [J].

Buetow, KH ;

Edmonson, MN ;

Cassidy, AB .

NATURE GENETICS, 1999, 21 (03) :323-325

[5] d2_cluster: A validated method for clustering EST and full-length cDNA sequences [J].

Burke, J ;

Davison, D ;

Hide, W .

GENOME RESEARCH, 1999, 9 (11) :1135-1142

[6] Characterization of single-nucleotide polymorphisms in coding regions of human genes [J].

Cargill, M ;

Altshuler, D ;

Ireland, J ;

Sklar, P ;

Ardlie, K ;

Patil, N ;

Lane, CR ;

Lim, EP ;

Kalyanaraman, N ;

Nemesh, J ;

Ziaugra, L ;

Friedland, L ;

Rolfe, A ;

Warrington, J ;

Lipshutz, R ;

Daley, GQ ;

Lander, ES .

NATURE GENETICS, 1999, 22 (03) :231-238

[7] Single nucleotide polymorphism (SNP) discovery in porcine expressed genes [J].

Fahrenkrug, SC ;

Freking, BA ;

Smith, TPL ;

Rohrer, GA ;

Keele, JW .

ANIMAL GENETICS, 2002, 33 (03) :186-195

[8]

Gu ZJ, 1998, HUM MUTAT, V12, P221, DOI 10.1002/(SICI)1098-1004(1998)12:4<221::AID-HUMU1>3.0.CO

[9]

2-I

[10] Estimation of DNA sequence diversity in bovine cytokine genes [J].

Heaton, MP ;

Grosse, WM ;

Kappes, SM ;

Keele, JW ;

Chitko-McKown, CG ;

Cundiff, LV ;

Braun, A ;

Little, DP ;

Laegreid, WW .

MAMMALIAN GENOME, 2001, 12 (01) :32-37

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