{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:05:39Z","timestamp":1773277539780,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3432,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge volumes of data create computational challenges in both memory consumption and CPU usage.<\/jats:p><jats:p>Results: We propose the complete composition vector representation for an HIV-1 strain, and a string scoring method to extract the nucleotide composition strings that contain the richest evolutionary information for phylogenetic analysis. In this way, a large-scale whole genome phylogenetic analysis for thousands of strains can be done both efficiently and effectively. By using 42 carefully curated strains as references, we apply our method to subtype 1156 HIV-1 strains (10.5 million nucleotides in total), which include 825 pure subtype strains and 331 recombinants. Our results show that our nucleotide composition string selection scheme is computationally efficient, and is able to define both pure subtypes and recombinant forms for HIV-1 strains using the 5000 top ranked nucleotide strings.<\/jats:p><jats:p>Availability: The Java executable and the HIV-1 datasets are accessible through \u2018http:\/\/www.cs.ualberta.ca\/~ghlin\/src\/WebTools\/hiv.php<\/jats:p><jats:p>Contact: \u00a0ghlin@cs.ualberta.ca<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm248","type":"journal-article","created":{"date-parts":[[2007,5,12]],"date-time":"2007-05-12T00:24:25Z","timestamp":1178929465000},"page":"1744-1752","source":"Crossref","is-referenced-by-count":43,"title":["Nucleotide composition string selection in HIV-1 subtyping using whole genomes"],"prefix":"10.1093","volume":"23","author":[{"given":"Xiaomeng","family":"Wu","sequence":"first","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]},{"given":"Zhipeng","family":"Cai","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]},{"given":"Xiu-Feng","family":"Wan","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]},{"given":"Tin","family":"Hoang","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]},{"given":"Randy","family":"Goebel","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]},{"given":"Guohui","family":"Lin","sequence":"additional","affiliation":[{"name":"1 Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada and 2Department of Microbiology, Miami University, Oxford, OH 45056, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,5,11]]},"reference":[{"key":"2023041105225509900_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023041105225509900_","first-page":"107","article-title":"A compression algorithm for DNA sequences and its applications in genome comparison","author":"Chen","year":"2000"},{"key":"2023041105225509900_","doi-asserted-by":"crossref","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences","volume":"21","author":"de Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"2023041105225509900_","doi-asserted-by":"crossref","first-page":"i116","DOI":"10.1093\/bioinformatics\/bth902","article-title":"Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species","volume":"20","author":"Dopazo","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041105225509900_","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1097\/01.aids.0000237368.64488.ae","article-title":"Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity","volume":"20","author":"Gifford","year":"2006","journal-title":"AIDS"},{"key":"2023041105225509900_","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1016\/0306-4573(94)90014-0","article-title":"A new challenge for compression algorithms: genetic sequences","volume":"30","author":"Grumbach","year":"1994","journal-title":"J. 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