Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree
作者： Jacqueline Batley , David Edwards
DOI: 10.1007/978-1-59745-251-9_15
关键词:
摘要: Molecular genetic markers represent one of the most powerful tools for analysis genomes and association heritable traits with underlying variation. The development high-throughput methods detection single nucleotide polymorphisms (SNPs) simple sequence repeats (SSRs) has led to a revolution in their use as molecular markers. availability large data sets permits mining these markers, which may then be used applications such trait mapping, diversity marker assisted selection agriculture. Here we describe web-based automated discovery SSRs using SSR taxonomy tree, SNPs from SNPServer identification validated within dbSNP database. tree identifies pre-determined amplification primers virtually all species represented GenBank uses redundancy based approach identify DNA sequences. Following Submission interest, BLAST similar sequences, CAP3 cluster assemble sequences SNP software autoSNP detect insertion/deletion (indel) polymorphisms. NCBI database is catalogue variation, hosting several public-domain archive.
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Mark D Adams, Anthony R Kerlavage, Robert D Fleischmann, Rebecca A Fuldner, Carol J Bult, Norman H Lee, Ewen F Kirkness, Keith G Weinstock, Jeannine D Gocayne, Owen White, None, Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature. ,vol. 377, pp. 3- 174 ,(1995)
Erica Logan, Christopher G Love, David Edwards, Jennifer C Mortimer, Jacqueline Batley, Simple sequence repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology. ,vol. 7, pp. 17- 25 ,(2005)
P. K. Gupta, M. Prasad, J. K. Roy, Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants Current Science Association. ,(2001)
Steve Rozen, Helen Skaletsky, Primer3 on the WWW for general users and for biologist programmers. Methods of Molecular Biology. ,vol. 132, pp. 365- 386 ,(2000) , 10.1385/1-59259-192-2:365
Kenneth H. Buetow, Michael N. Edmonson, Anna B. Cassidy, Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genetics. ,vol. 21, pp. 323- 325 ,(1999) , 10.1038/6851
K.J. Edwards, J.H.A. Barker, A. Daly, C. Jones, A. Karp, Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques. ,vol. 20, pp. 758- 760 ,(1996) , 10.2144/96205BM04
Stephen T. Sherry, Minghong Ward, Karl Sirotkin, dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Research. ,vol. 9, pp. 677- 679 ,(1999) , 10.1101/GR.9.8.677
Wayne Powell, Jim Provan, Gordon C. Machray, Polymorphism revealed by simple sequence repeats Trends in Plant Science. ,vol. 1, pp. 215- 222 ,(1996) , 10.1016/1360-1385(96)86898-1
Mukund V. Katti, Prabhakar K. Ranjekar, Vidya S. Gupta, Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences Molecular Biology and Evolution. ,vol. 18, pp. 1161- 1167 ,(2001) , 10.1093/OXFORDJOURNALS.MOLBEV.A003903
Ann-Christine Syvänen, Accessing genetic variation: genotyping single nucleotide polymorphisms Nature Reviews Genetics. ,vol. 2, pp. 930- 942 ,(2001) , 10.1038/35103535