{"title":"OligoSpecificitySystem: global matching efficiency calculation of oligonucleotide sets taking into account degeneracy and mismatch possibilities.","authors":"R J Michelland, S Combes, L Cauquil","doi":"10.1504/ijdmb.2014.062148","DOIUrl":null,"url":null,"abstract":"<p><p>Oligonucleotide sets are widely used in molecular biology to target a group of nucleic acid sequences using Polymerase Chain Reaction (PCR)-based technologies. Currently, the global matching efficiency of an oligonucleotide set is considered to be equal to the lower matching efficiency calculated for each oligonucleotide. However, sequences matching the limiting oligonucleotide did not always match the other oligonucleotide of the set, resulting in a biased evaluation of the matching efficiency. The OligoSpecificitySystem program avoid this bias by calculations of the real global matching efficiency of oligonucleotide sets. It can process all kinds of oligonucleotide sets, including the number of oligonucleotides, base pair degeneracy occurrences or mismatch occurrences.</p>","PeriodicalId":54964,"journal":{"name":"International Journal of Data Mining and Bioinformatics","volume":"9 4","pages":"417-23"},"PeriodicalIF":0.2000,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/ijdmb.2014.062148","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Journal of Data Mining and Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1504/ijdmb.2014.062148","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 1
Abstract
Oligonucleotide sets are widely used in molecular biology to target a group of nucleic acid sequences using Polymerase Chain Reaction (PCR)-based technologies. Currently, the global matching efficiency of an oligonucleotide set is considered to be equal to the lower matching efficiency calculated for each oligonucleotide. However, sequences matching the limiting oligonucleotide did not always match the other oligonucleotide of the set, resulting in a biased evaluation of the matching efficiency. The OligoSpecificitySystem program avoid this bias by calculations of the real global matching efficiency of oligonucleotide sets. It can process all kinds of oligonucleotide sets, including the number of oligonucleotides, base pair degeneracy occurrences or mismatch occurrences.
期刊介绍：
Mining bioinformatics data is an emerging area at the intersection between bioinformatics and data mining. The objective of IJDMB is to facilitate collaboration between data mining researchers and bioinformaticians by presenting cutting edge research topics and methodologies in the area of data mining for bioinformatics. This perspective acknowledges the inter-disciplinary nature of research in data mining and bioinformatics and provides a unified forum for researchers/practitioners/students/policy makers to share the latest research and developments in this fast growing multi-disciplinary research area.
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