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Online Journal of Bioinformatics ©
Volume 12(1):34-45, 2011
In Silico mining of single nucleotide polymorphisms in expressed sequence tags dataset of Allium cepa L.
Radhika V1, Reddy DCL, Bhardwaj A, Aswath C2
Division of Biotechnology, Indian Institute of Horticultural Research, Hessaraghatta Lake, Bangalore , India
Radhika V, Reddy DCL, Bhardwaj A, Aswath C, In Silico mining of single nucleotide polymorphisms in expressed sequence tags dataset of Allium cepa L., Online J Bioinformatics, 12(1):18-33, 2011. Single nucleotide polymorphisms (SNPs) are abundant in plant genomes and are thus used frequently in genetic analysis and crop breeding programs. Potential SNPs from expressed sequence tags (ESTs) of Allium cepa were mined for a total of 232 potential SNPs identified from 20,157 ESTs from NCBI. The SNPs occurred on an average frequency of 1 per 57 bp in the EST sequences. The ratio of transitions to transversions was 1.7: 1, and 65 of the 232 SNP sites were cut by different restriction enzymes. Primers could be designed for 227 SNPs and used for onion breeding programs after validation in wet lab.
Keywords: Cap3, contig, SNPDigger, transition, transversion