{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T01:41:48Z","timestamp":1771551708477,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,7]],"date-time":"2018-03-07T00:00:00Z","timestamp":1520380800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100003500","name":"University of Padova","doi-asserted-by":"publisher","award":["CPDA138081\/13"],"award-info":[{"award-number":["CPDA138081\/13"]}],"id":[{"id":"10.13039\/501100003500","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed NeSSie, an easily customizable C\/C++\u200964-bit library and tool, based on dynamic programming, to quickly scan for perfect and degenerate DNA palindromes, mirrors and potential triplex forming patterns. In addition, the tool computes linguistic complexity and Shannon entropy measures to verify the repetitive nature of the DNA regions enriched in these motifs. As a case study, the analysis of the Mycobacterium bovis genome is presented.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/www.medcomp.medicina.unipd.it\/main_site\/doku.php? id=nessie and https:\/\/github.com\/B3rse\/nessie<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty142","type":"journal-article","created":{"date-parts":[[2018,3,7]],"date-time":"2018-03-07T04:10:38Z","timestamp":1520395838000},"page":"2503-2505","source":"Crossref","is-referenced-by-count":17,"title":["NeSSie: a tool for the identification of approximate DNA sequence symmetries"],"prefix":"10.1093","volume":"34","author":[{"given":"Michele","family":"Berselli","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine, University of Padova, Padova, Italy"}]},{"given":"Enrico","family":"Lavezzo","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Padova, Padova, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0246-3119","authenticated-orcid":false,"given":"Stefano","family":"Toppo","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, University of Padova, Padova, Italy"}]}],"member":"286","published-online":{"date-parts":[[2018,3,7]]},"reference":[{"key":"2023012713012154600_bty142-B1","doi-asserted-by":"crossref","first-page":"3591","DOI":"10.1021\/jacs.6b10786","article-title":"Structure of a stable G-hairpin","volume":"139","author":"Gajarsky","year":"2017","journal-title":"J. Am. Chem. Soc"},{"key":"2023012713012154600_bty142-B2","doi-asserted-by":"crossref","first-page":"3373","DOI":"10.1093\/bioinformatics\/btx413","article-title":"pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R","volume":"33","author":"Hon","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012713012154600_bty142-B3","doi-asserted-by":"crossref","first-page":"3511","DOI":"10.1093\/nar\/gkl456","article-title":"Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human beta-globin gene cluster","volume":"34","author":"Kaushik","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023012713012154600_bty142-B4","doi-asserted-by":"crossref","first-page":"2510","DOI":"10.1093\/bioinformatics\/btr439","article-title":"A dynamic programming algorithm for identification of triplex-forming sequences","volume":"27","author":"Lexa","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012713012154600_bty142-B5","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/bab.1266","article-title":"An overview to understand the role of PE_PGRS family proteins in mycobacterium tuberculosis H37 Rv and their potential as new drug targets","volume":"62","author":"Meena","year":"2015","journal-title":"Biotechnol. Appl. Biochem"},{"key":"2023012713012154600_bty142-B6","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"2023012713012154600_bty142-B7","volume-title":"DNA Structure and Function","author":"Sinden","year":"1994"},{"key":"2023012713012154600_bty142-B8","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1016\/S0021-9258(19)57268-4","article-title":"Unusual DNA structures","volume":"263","author":"Wells","year":"1988","journal-title":"J. Biol. Chem"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2503\/48917572\/bioinformatics_34_14_2503.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2503\/48917572\/bioinformatics_34_14_2503.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:52:04Z","timestamp":1674827524000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/14\/2503\/4924217"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,3,7]]},"references-count":8,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2018,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty142","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,15]]},"published":{"date-parts":[[2018,3,7]]}}}