{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T03:31:32Z","timestamp":1764905492665},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences.<\/jats:p>\n               <jats:p>Results: Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify cis-regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics.<\/jats:p>\n               <jats:p>Availability: Our implementation of the five statistics is available as R package named \u2018multiAlignFree\u2019 at be http:\/\/www-rcf.usc.edu\/\u223cfsun\/Programs\/multiAlignFree\/multiAlignFreemain.html.<\/jats:p>\n               <jats:p>Contact: \u00a0reinert@stats.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt462","type":"journal-article","created":{"date-parts":[[2013,8,30]],"date-time":"2013-08-30T00:39:04Z","timestamp":1377823144000},"page":"2690-2698","source":"Crossref","is-referenced-by-count":10,"title":["Multiple alignment-free sequence comparison"],"prefix":"10.1093","volume":"29","author":[{"given":"Jie","family":"Ren","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minghua","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gesine","family":"Reinert","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,8,29]]},"reference":[{"key":"2023063010275440700_btt462-B1","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1093\/bioinformatics\/btq358","article-title":"An alignment-free method to identify candidate orthologous enhancers in multiple drosophila genomes","volume":"26","author":"Arunachalam","year":"2010","journal-title":"Bioinformatics"},{"key":"2023063010275440700_btt462-B2","doi-asserted-by":"crossref","first-page":"5155","DOI":"10.1073\/pnas.83.14.5155","article-title":"A measure of the similarity of sets of sequences not requiring sequence alignment","volume":"83","author":"Blaisdell","year":"1986","journal-title":"Proc. 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