TY - CHAP
T1 - Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers
AU - Batley, Jacqueline
AU - Jewell, Erica
AU - Edwards, David
PY - 2007/11/1
Y1 - 2007/11/1
N2 - Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last, decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern, genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait, mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data, SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.
AB - Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last, decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern, genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait, mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data, SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.
KW - AutoSNP
KW - Microsatellite
KW - Molecular genetic marker
KW - Simple sequence repeat
KW - Single nucleotide polymorphism
KW - SNPServer
KW - SSR taxonomy tree
KW - SSRPrimer
UR - http://www.scopus.com/inward/record.url?scp=40549128392&partnerID=8YFLogxK
U2 - 10.1007/978-1-59745-535-0_23
DO - 10.1007/978-1-59745-535-0_23
M3 - Chapter
C2 - 18287708
AN - SCOPUS:40549128392
SN - 9781597455350
T3 - Methods in Molecular Biology
SP - 473
EP - 494
BT - Plant Bioinformatics - Methods and Protocols
PB - Humana Press
ER -