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Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code and test data are available from https:\/\/gitlab.ub.uni-bielefeld.de\/gi\/plast.<\/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\/btab077","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T16:30:48Z","timestamp":1611851448000},"page":"2266-2274","source":"Crossref","is-referenced-by-count":10,"title":["Detecting high-scoring local alignments in pangenome graphs"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0744-7078","authenticated-orcid":false,"given":"Tizian","family":"Schulz","sequence":"first","affiliation":[{"name":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615, Germany"},{"name":"Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University , Bielefeld 33615, Germany"},{"name":"Graduate School \u2018Digital Infrastructure for the Life Sciences\u2019 (DILS), Bielefeld University , Bielefeld 33615, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2249-9880","authenticated-orcid":false,"given":"Roland","family":"Wittler","sequence":"additional","affiliation":[{"name":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615, Germany"},{"name":"Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University , Bielefeld 33615, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8536-6065","authenticated-orcid":false,"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[{"name":"Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen 45122, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1143-0172","authenticated-orcid":false,"given":"Faraz","family":"Hach","sequence":"additional","affiliation":[{"name":"Vancouver Prostate Centre , Vancouver, BC V6H 3Z6, Canada"},{"name":"Department of Urologic Sciences, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4656-7155","authenticated-orcid":false,"given":"Jens","family":"Stoye","sequence":"additional","affiliation":[{"name":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University , Bielefeld 33615, Germany"},{"name":"Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University , Bielefeld 33615, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,3]]},"reference":[{"key":"2023051609141918900_btab077-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023051609141918900_btab077-B2","doi-asserted-by":"crossref","first-page":"e1007261","DOI":"10.1371\/journal.pgen.1007261","article-title":"A genomic overview of the population structure of Salmonella","volume":"14","author":"Alikhan","year":"2018","journal-title":"PLOS Genet"},{"key":"2023051609141918900_btab077-B3","volume-title":"17th International Workshop on Algorithms in Bioinformatics (WABI 2017)","author":"Almodaresi","year":"2017"},{"key":"2023051609141918900_btab077-B4","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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