Author: Lee, Charlie Wah Heng; Koh, Chee Wee; Chan, Yang Sun; Aw, Pauline Poh Kim; Loh, Kuan Hon; Han, Bing Ling; Thien, Pei Ling; Nai, Geraldine Yi Wen; Hibberd, Martin L.; Wong, Christopher W.; Sung, Wing-Kin
Title: Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays Document date: 2010_2_25
ID: 1rhy8td0_10
Snippet: We found 36 mutation hotspots in the alignments where mutations occurred near one another (within 20 bp). A perfect match (PM) probe residing in a mutation hotspot may contain mismatches that will have a detrimental effect on its hybridization intensity. To avoid this problem, we designed additional PM probes that contain all possible combinations of mutations found in each mutation hotspot. Thus, if two mutations are found within 20 bp of each o.....
Document: We found 36 mutation hotspots in the alignments where mutations occurred near one another (within 20 bp). A perfect match (PM) probe residing in a mutation hotspot may contain mismatches that will have a detrimental effect on its hybridization intensity. To avoid this problem, we designed additional PM probes that contain all possible combinations of mutations found in each mutation hotspot. Thus, if two mutations are found within 20 bp of each other in the alignments, then we need in total four (2 2 ) PM probes to encode them. In general, 2 x PM probes are needed to completely encode a cluster of x mutations that occur within 20 bp of one another in the alignments.
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