{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T21:23:00Z","timestamp":1717708980404},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Hybridization of oligonucleotides with longer nucleotide sequences is an essential step in nucleic acid biosynthesis in vitro and in vivo, in oligonucleotide-based diagnostics, and in therapeutic applications of oligonucleotides. A major factor determining sensitivity and selectivity of hybridization is the number of base pair mismatches that occur in an ungapped alignment of the oligonucleotide (probe) and a longer sequence (target).<\/jats:p>\n               <jats:p>Results: The k-distance match count between the probe and the target is defined as the number of ungapped alignments between the two sequences that have exactly k mismatches, and the k-neighbor match count is defined as the sum of the j-distance match counts for j between 0 and k. We derive a novel formula for the probability of a k-distance match. This formula is based on the assumption that the target is strand-symmetric Bernoulli text (i.e. nucleotides are independently, identically distributed in the target and satisfy Chargaff's second parity rule). Our model predicts that the GC-content in both the probe and the target significantly affects the match count expectation. The ratio of k-neighbor match counts in two distinct genomes for a given probe is a measure of its specificity. We calculated such ratios for pairs of bacterial genomes with different combinations of length, GC-content and phylogenetic distance. Examination of the extreme values of these ratios indicates that probes with a high discriminative power exist for each tested pair.<\/jats:p>\n               <jats:p>Supplementary information: Stowers Institute Technical Report No. 0002, C++ source code, Mathematica notebooks and other information is available at http:\/\/www.stowers-institute.org\/labs\/bioinformatics\/omm\/index.htm<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg374","type":"journal-article","created":{"date-parts":[[2003,12,23]],"date-time":"2003-12-23T16:57:44Z","timestamp":1072198664000},"page":"67-74","source":"Crossref","is-referenced-by-count":4,"title":["Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes"],"prefix":"10.1093","volume":"20","author":[{"given":"O. Michael","family":"Melko","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arcady R.","family":"Mushegian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,1,1]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/1\/67\/48905093\/bioinformatics_20_1_67.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/1\/67\/48905093\/bioinformatics_20_1_67.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:47:40Z","timestamp":1674672460000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/1\/67\/228886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,1,1]]},"references-count":0,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2004,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg374","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,1,1]]},"published":{"date-parts":[[2004,1,1]]}}}