… permanently leading to errors – the plus \/ minus strand orientation and the consecutive sequence \/ allele designation of SNPs. Only recently I came across a fancy way how to define strand direction – from a tech note by Illumina that deserves a larger audience. They introduce a TOP\/BOTTOM strand concept instead of PLUS\/MINUS.
\nLet us consider the case where one allele is A and the remaining variation a C or G. In this instance, the sequence direction is defined TOP and allele 1 as A while allele 2 is C or G. Similar with T and variation C or G: the direction is BOTTOM, allele 1 = A, and allele 2 = C or G. If the SNP is an [A\/T] or a [C\/G], however, then these rules do not apply. <\/p>\n
\nFor the [A\/T] SNP, the presence of an A would indicate TOP and the presence of a T would indicate BOTTOM. But, both the A and the T would be designated as allele 1 resulting in ambiguity. It would be similarly confusing to attempt to designate strand and allele for the [C\/G] SNP. These [A\/T] and [C\/G] pairings are considered ambiguous for the purpose of determining strand and allele based on the SNP alone. Illumina employs a \u00e2\u20ac\u02dcsequence walking\u00e2\u20ac\u2122 technique to designate strand and allele for [A\/T] and [C\/G] SNPs. For this sequence walking method, the actual SNP is considered to be position \u00e2\u20ac\u02dcn\u00e2\u20ac\u2122. The sequences immediately before and after the SNP are \u00e2\u20ac\u02dcn-1\u00e2\u20ac\u2122 and \u00e2\u20ac\u02dcn+1\u00e2\u20ac\u2122, respectively. Similarly, two base pairs before the SNP is \u00e2\u20ac\u02dcn-2\u00e2\u20ac\u2122 and two base pairs after the SNP is \u00e2\u20ac\u02dcn+2\u00e2\u20ac\u2122, etc. Using this method, sequence walking continues until an unambiguous* pairing is present […] To designate strand, when the A or T in the first unambiguous pair is on the 5\u00e2\u20ac\u2122 side of the SNP, then the sequence is designated TOP. When the A or T in the first unambiguous pair is on the 3\u00e2\u20ac\u2122 side of the SNP, then the sequence is designated BOTTOM. To designate allele for an [A\/T] SNP, when the strand is TOP then allele 1 = A and allele 2 = T. When the strand is BOTTOM, then allele 1 = T and allele 2 = A.\n<\/p><\/blockquote>\n
The only point that I do not understand – the 5′ ends with a terminal phosphate group and the 3′ end with a terminal hydroxyl group – where is the hen and where is the egg if I have an unknown sequence?<\/p>\n\n
<\/p>\n
\n CC-BY-NC Science Surf , accessed 19.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"… permanently leading to errors – the plus \/ minus strand orientation and the consecutive sequence \/ allele designation of SNPs. Only recently I came across a fancy way how to define strand direction – from a tech note CC-BY-NC Science Surf , accessed 19.04.2026<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2,9],"tags":[1852,1855,1853,207,1851,1854],"class_list":["post-1562","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","category-computer-software","tag-base-pairs","tag-presence","tag-sequences","tag-snp","tag-strand-direction","tag-variation"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1562","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=1562"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1562\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=1562"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=1562"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=1562"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}