{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T17:31:27Z","timestamp":1746207087708},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2017,6,15]],"date-time":"2017-06-15T00:00:00Z","timestamp":1497484800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,1]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package \u2018kmerPyramid\u2019 that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid\u2019s axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The \u2018kmerPyramid\u2019 can particularly be used for visualization of intra- and inter species differences.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The R-package \u2018kmerPyramid\u2019 is available from the GitHub website at https:\/\/github.com\/jkruppa\/kmerPyramid.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx385","type":"journal-article","created":{"date-parts":[[2017,6,12]],"date-time":"2017-06-12T11:08:36Z","timestamp":1497265716000},"page":"3115-3116","source":"Crossref","is-referenced-by-count":2,"title":["kmerPyramid: an interactive visualization tool for nucleobase and k<\/i>-mer frequencies"],"prefix":"10.1093","volume":"33","author":[{"given":"Jochen","family":"Kruppa","sequence":"first","affiliation":[{"name":"Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Erhard","family":"van der Vries","sequence":"additional","affiliation":[{"name":"Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Wendy K","family":"Jo","sequence":"additional","affiliation":[{"name":"Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Alexander","family":"Postel","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Paul","family":"Becher","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Albert","family":"Osterhaus","sequence":"additional","affiliation":[{"name":"Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany"}]},{"given":"Klaus","family":"Jung","sequence":"additional","affiliation":[{"name":"Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,6,15]]},"reference":[{"key":"2023020206472115400_btx385-B1","doi-asserted-by":"crossref","first-page":"1854.","DOI":"10.1038\/ncomms2884","article-title":"Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage","volume":"4","author":"Dodsworth","year":"2013","journal-title":"Nat. Commun"},{"key":"2023020206472115400_btx385-B2","doi-asserted-by":"crossref","first-page":"e603","DOI":"10.7717\/peerj.603","article-title":"GroopM: an automated tool for the recovery of population genomes from related metagenomes","volume":"2","author":"Imelfort","year":"2014","journal-title":"PeerJ"},{"key":"2023020206472115400_btx385-B3","doi-asserted-by":"crossref","first-page":"9.","DOI":"10.1186\/1745-6150-8-9","article-title":"Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park","volume":"8","author":"Podar","year":"2013","journal-title":"Biol. Direct"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3115\/49041466\/bioinformatics_33_19_3115.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/19\/3115\/49041466\/bioinformatics_33_19_3115.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:47:37Z","timestamp":1675320457000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/19\/3115\/3868723"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,6,15]]},"references-count":3,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2017,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx385","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,10,1]]},"published":{"date-parts":[[2017,6,15]]}}}