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An interactive bovine in silico SNP database (IBISS)

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Abstract

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 IBISS 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.

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References

  • SF Altschul TL Madden AA Schaffer J Zhang Z Zhang et al. (1997) ArticleTitleGapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389–3402 Occurrence Handle1:CAS:528:DyaK2sXlvFyhu7w%3D Occurrence Handle9254694

    CAS  PubMed  Google Scholar 

  • MR Band JH Larson M Rebeiz CA Green DW Heyen et al. (2000) ArticleTitleAn ordered comparative map of the cattle and human genomes Genome Res 10 1359–1368 Occurrence Handle10.1101/gr.145900 Occurrence Handle1:CAS:528:DC%2BD3cXms1yjur4%3D Occurrence Handle10984454

    Article  CAS  PubMed  Google Scholar 

  • W Barendse D Vaiman SJ Kemp Y Sugimoto SM Armitage et al. (1997) ArticleTitleA medium-density genetic linkage map of the bovine genome Mamm Genome 8 21–28 Occurrence Handle10.1007/s003359900340 Occurrence Handle1:CAS:528:DyaK2sXnsVOgsw%3D%3D Occurrence Handle9021143

    Article  CAS  PubMed  Google Scholar 

  • KH Buetow MN Edmonson AB Cassidy (1999) ArticleTitleReliable identification of large numbers of candidate SNPs from public EST data Nat Genet 21 323–325 Occurrence Handle10.1038/6851 Occurrence Handle1:CAS:528:DyaK1MXitVCitb0%3D Occurrence Handle10080189

    Article  CAS  PubMed  Google Scholar 

  • J Burke D Davison W Hide (1999) ArticleTitleD2_cluster: A validated method for clustering EST and full-length cDNA sequences Genome Res 9 1135–1142 Occurrence Handle10.1101/gr.9.11.1135 Occurrence Handle1:CAS:528:DyaK1MXns12kt7w%3D Occurrence Handle10568753

    Article  CAS  PubMed  Google Scholar 

  • M Cargill D Altshuler P Sklar K Ardlie N Patil et al. (1999) ArticleTitleCharacterisation of single nucleotide polymorphisms in coding regions of human genes Nat Genet 22 231–238 Occurrence Handle10.1038/10290 Occurrence Handle1:CAS:528:DyaK1MXkt1eqsb4%3D Occurrence Handle10391209

    Article  CAS  PubMed  Google Scholar 

  • SC Fahrenkrug BA Freking TPL Smith GA Rohrer JW Keele (2002) ArticleTitleSingle nucleotide polymorphism (SNP) discovery in porcine expressed genes Anim Genet 33 186–195 Occurrence Handle10.1046/j.1365-2052.2002.00846.x Occurrence Handle1:CAS:528:DC%2BD38Xlt1Kjs7g%3D Occurrence Handle12030921

    Article  CAS  PubMed  Google Scholar 

  • Z Gu LD Hillier P-Y Kwok (1998) ArticleTitleSingle nucleotide polymorphism hunting in cyberspace Hum Mutat 12 221–225 Occurrence Handle10.1002/(SICI)1098-1004(1998)12:4<221::AID-HUMU1>3.0.CO;2-I Occurrence Handle1:CAS:528:DyaK1cXmtFWqsr4%3D Occurrence Handle9744471

    Article  CAS  PubMed  Google Scholar 

  • MP Heaton WM Grosse SM Kappes JW Keele GC Chitko-Mckown et al. (2001) ArticleTitleEstimation of DNA sequence diversity in bovine cytokine genes Mamm Genome 12 32–37 Occurrence Handle10.1007/s003350010223 Occurrence Handle1:CAS:528:DC%2BD3MXptlGqtA%3D%3D Occurrence Handle11178741

    Article  CAS  PubMed  Google Scholar 

  • R Holliday GW Grigg (1993) ArticleTitleDNA methylation and mutation Mutat Res 285 61–67 Occurrence Handle1:CAS:528:DyaK3sXhtF2js78%3D Occurrence Handle7678134

    CAS  PubMed  Google Scholar 

  • G Hu B Modrek HMFR Stensland J Saarela P Pajukanta et al. (2002) ArticleTitleEfficient discovery of single-nucleotide polymorphisms in coding regions of human genes Pharmacogenomics J 2 236–242 Occurrence Handle10.1038/sj.tpj.6500109 Occurrence Handle1:CAS:528:DC%2BD38XmsVGmu74%3D Occurrence Handle12196912

    Article  CAS  PubMed  Google Scholar 

  • X Huang J Zhang (1996) ArticleTitleMethods for comparing a DNA sequence with a protein sequence Comput Applic Biosci 12 497–506 Occurrence Handle1:CAS:528:DyaK2sXhtlWkt7k%3D

    CAS  Google Scholar 

  • K Irizarry V Kustanovich C Li N Brown S Nelson et al. (2000) ArticleTitleGenome-wide analysis of single nucleotide polymorphisms in human expressed sequences Nat Genet 26 233–236 Occurrence Handle10.1038/79981 Occurrence Handle1:CAS:528:DC%2BD3cXntlGmsLs%3D Occurrence Handle11017085

    Article  CAS  PubMed  Google Scholar 

  • C Iseli CV Jongeneel P Bucher (1999) ArticleTitleESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences Proc Int Conf Intell Syst Mol Biol 1 38–48

    Google Scholar 

  • SM Kappes JW Keele RT Stone RA McGraw TS Sonstegard et al. (1997) ArticleTitleA second-generation linkage map of the bovine genome Genome Res 7 235–249 Occurrence Handle1:CAS:528:DyaK2sXhvFamsbo%3D Occurrence Handle9074927

    CAS  PubMed  Google Scholar 

  • D Karolchik R Baertsch M Diekhans TS Furey A Hinrichs et al. (2003) ArticleTitleThe UCSC Genome Browser Database Nucleic Acids Res 31 51–54 Occurrence Handle10.1093/nar/gkg129 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSgu7g%3D Occurrence Handle12519945

    Article  CAS  PubMed  Google Scholar 

  • WJ Kent (2002) ArticleTitleBLAT—The BLAST-Like Alignment Tool Genome Res 12 656–664 Occurrence Handle1:CAS:528:DC%2BD38XivVemtLw%3D Occurrence Handle11932250

    CAS  PubMed  Google Scholar 

  • H Kim C Schmidt KS Decker MG Emara (2003) ArticleTitleA double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data Anim Genet 34 249–254 Occurrence Handle10.1046/j.1365-2052.2003.01003.x Occurrence Handle1:CAS:528:DC%2BD3sXovFCht7c%3D Occurrence Handle12873212

    Article  CAS  PubMed  Google Scholar 

  • L Kruglyak (1997) ArticleTitleThe use of a genetic map of biallelic markers in linkage studies Nat Genet 17 21–24

    Google Scholar 

  • K Lindblad–Toh E Winchester M Daly DG Wang JN Hirschhorn et al. (2000) ArticleTitleLarge-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse Nat Genet 24 381–386 Occurrence Handle10.1038/74215 Occurrence Handle1:CAS:528:DC%2BD3cXisVCjsbg%3D Occurrence Handle10742102

    Article  CAS  PubMed  Google Scholar 

  • C Lottaz C Iseli CV Jongeneel P Bucher (2003) ArticleTitleModeling sequencing errors by combining Hidden Markov models Bioinformatics 19 103–112 Occurrence Handle10.1093/bioinformatics/btg1067

    Article  Google Scholar 

  • RT Miller AG Christoffels C Gopalakrishnan J Burke AA Ptitsyn et al. (1999) ArticleTitleA comprehensive approach to clustering of expressed human gene sequence: The Sequence Tag Alignment and Consensus Knowledgebase Genome Res 9 1143–1155 Occurrence Handle10.1101/gr.9.11.1143 Occurrence Handle1:CAS:528:DyaK1MXns12kt70%3D Occurrence Handle10568754

    Article  CAS  PubMed  Google Scholar 

  • J Muilu P Rodriguez–Tome A Robinson (2001) ArticleTitleGbuil-der—an application for the visualization and integration of EST cluster data Genome Res 11 179–184 Occurrence Handle10.1101/gr.157501 Occurrence Handle1:CAS:528:DC%2BD3MXmsVCqsg%3D%3D Occurrence Handle11156627

    Article  CAS  PubMed  Google Scholar 

  • JC Mullikin SE Hunt CG Cole BJ Mortimore CM Rice et al. (2000) ArticleTitleAn SNP map of human chromosome 22 Nature 407 516–520 Occurrence Handle10.1038/35035089 Occurrence Handle1:CAS:528:DC%2BD3cXntlSks7w%3D Occurrence Handle11029003

    Article  CAS  PubMed  Google Scholar 

  • J Parkinson DB Guiliano M Blaxter (2002) ArticleTitleMaking sense of EST sequences by CLOBBing them Bioinformatics 3 31 Occurrence Handle10.1186/1471-2105-3-31 Occurrence Handle12398795

    Article  PubMed  Google Scholar 

  • WR Pearson T Wood Z Zhang W Miller (1997) ArticleTitleComparison of DNA sequences with protein sequences Genomics 46 24–36 Occurrence Handle10.1006/geno.1997.4995 Occurrence Handle1:CAS:528:DyaK2sXnvVCkur8%3D Occurrence Handle9403055

    Article  CAS  PubMed  Google Scholar 

  • L Picoult–Newberg TE Ideker MG Pohl SL Taylor MA Donaldson et al. (1999) ArticleTitleMining SNPs from EST databases Genome Res 9 167–174 Occurrence Handle1:CAS:528:DyaK1MXhsFyjtLc%3D Occurrence Handle10022981

    CAS  PubMed  Google Scholar 

  • S Rozen HJ Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers S Krawetz S Misener (Eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology Humana Press Totowa, NJ pp 365–386

    Google Scholar 

  • RT Stone WM Grosse E Casas TPL Smith JW Keel et al. (2002) ArticleTitleUse of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers Mamm Genome 13 211–215 Occurrence Handle10.1007/s00335-001-2124-9 Occurrence Handle1:CAS:528:DC%2BD38XjtFymt7s%3D Occurrence Handle11956765

    Article  CAS  PubMed  Google Scholar 

  • P Taillon–Miller Z Gu Q Li LD Hillier P-Y Kwok (1998) ArticleTitleOverlapping genomic sequences: A treasure trove of single nucleotide polymorphisms Genome Res 8 748–754 Occurrence Handle1:CAS:528:DyaK1cXltFeltr0%3D Occurrence Handle9685323

    CAS  PubMed  Google Scholar 

  • GA Thorisson LD Stein (2003) ArticleTitleThe SNP consortium website: past, present and future Nucleic Acids Res 31 124–127 Occurrence Handle10.1093/nar/gkg052 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSnsL0%3D Occurrence Handle12519964

    Article  CAS  PubMed  Google Scholar 

  • HT Toivonen P Onkamo K Vasko V Ollikainen P Sevon et al. (2000) ArticleTitleData mining applied to linkage disequilibrium mapping Am J Hum Genet 67 133–145 Occurrence Handle10.1086/302954 Occurrence Handle1:CAS:528:DC%2BD3cXntVyks74%3D Occurrence Handle10848493

    Article  CAS  PubMed  Google Scholar 

  • W Upton HM Burrow A Dundon DL Robbinson EB Farrell (2001) ArticleTitleCRC breeding program design, measurement and database; methods that underpin CRC research results Aust J Exp Agr 41 943–952 Occurrence Handle10.1071/EA00064

    Article  Google Scholar 

  • A Vignal D Milan M San Crisobal A Eggen (2002) ArticleTitleA review on SNP and other types of molecular markers and their use in animal genetics Genet Sel Evol 34 275–305 Occurrence Handle10.1051/gse:2002009 Occurrence Handle1:CAS:528:DC%2BD38Xmt1Gmur0%3D Occurrence Handle12081799

    Article  CAS  PubMed  Google Scholar 

  • JL Weber EW Myers (1997) ArticleTitleHuman whole-genome shotgun sequencing Genome Res 7 401–409 Occurrence Handle1:CAS:528:DyaK2sXjtFWlsbY%3D Occurrence Handle9149936

    CAS  PubMed  Google Scholar 

  • FAO Werner G Durstewitz FA Habermann G Thaller W Krämer et al. (2004) ArticleTitleDetection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds Anim Genet 35 44–49 Occurrence Handle10.1111/j.1365-2052.2004.01123.x Occurrence Handle1:CAS:528:DC%2BD2cXitVKlsbk%3D Occurrence Handle14731229

    Article  CAS  PubMed  Google Scholar 

  • Z Yang GK-S Wong MA Eberle M Kibukawa DA Passey et al. (2000) ArticleTitleSampling SNPs Nat Genet 26 13–14 Occurrence Handle10.1038/81559 Occurrence Handle1:CAS:528:DC%2BD3cXmsVKkur8%3D

    Article  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank the entire Bioinformatics team at CSIRO LI and the staff at Electric Genetics for their assistance in using StackPACK to cluster these sequences. The authors also thank Bill Barendse and James Kijas for helpful and insightful discussions regarding specific areas of this paper. We thank Bill Barendse for cattle DNA samples and access to an ABI 377 DNA sequencer.

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Authors and Affiliations

  1. Queensland Bioscience Precinct, CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Australia

    Rachel J. Hawken, Wesley C. Barris, Sean M. McWilliam & Brian P. Dalrymple

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  1. Rachel J. Hawken
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  2. Wesley C. Barris
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  3. Sean M. McWilliam
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  4. Brian P. Dalrymple
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Correspondence to Rachel J. Hawken.

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Hawken, R.J., Barris, W.C., McWilliam, S. et al. An interactive bovine in silico SNP database (IBISS). Mamm Genome 15, 819–827 (2004). https://doi.org/10.1007/s00335-004-2382-4

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