Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design |
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| Authors: | Helen I Field Serena A Scollen Craig Luccarini Caroline Baynes Jonathan Morrison Alison M Dunning Douglas F Easton and Paul DP Pharoah |
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| Institution: | (1) Departments of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK;(2) Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK;(3) Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK |
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| Abstract: | Background In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their
sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences
flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for
repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. |
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