{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:39:45Z","timestamp":1706812785830},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential.<\/jats:p>\n In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify &gt;175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction.<\/jats:p>\n Availability and implementation: The source code can be downloaded at http:\/\/www.heiderlab.de<\/jats:p>\n Contact: \u00a0d.heider@wz-straubing.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu535","type":"journal-article","created":{"date-parts":[[2014,8,15]],"date-time":"2014-08-15T05:12:51Z","timestamp":1408079571000},"page":"3272-3273","source":"Crossref","is-referenced-by-count":8,"title":["gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing"],"prefix":"10.1093","volume":"30","author":[{"given":"Michael","family":"Olejnik","sequence":"first","affiliation":[{"name":"1 Institute of Computer Science, University of Muenster, 48149 Muenster and 2 Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michel","family":"Steuwer","sequence":"additional","affiliation":[{"name":"1 Institute of Computer Science, University of Muenster, 48149 Muenster and 2 Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergei","family":"Gorlatch","sequence":"additional","affiliation":[{"name":"1 Institute of Computer Science, University of Muenster, 48149 Muenster and 2 Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominik","family":"Heider","sequence":"additional","affiliation":[{"name":"1 Institute of Computer Science, University of Muenster, 48149 Muenster and 2 Department of Bioinformatics, University of Applied Sciences Weihenstephan-Triesdorf, 94315 Straubing, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,8,13]]},"reference":[{"key":"2023012711591830000_btu535-B1","doi-asserted-by":"crossref","first-page":"e49602","DOI":"10.1371\/journal.pone.0049602","article-title":"Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism","volume":"7","author":"Archer","year":"2012","journal-title":"PLoS One"},{"key":"2023012711591830000_btu535-B2","doi-asserted-by":"crossref","first-page":"e1002977","DOI":"10.1371\/journal.pcbi.1002977","article-title":"Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage","volume":"9","author":"Bozek","year":"2013","journal-title":"PLoS Comput. Biol."},{"key":"2023012711591830000_btu535-B3","doi-asserted-by":"crossref","first-page":"e1000743","DOI":"10.1371\/journal.pcbi.1000743","article-title":"Prediction of co-receptor usage of HIV-1 from genotype","volume":"6","author":"Dybowski","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023012711591830000_btu535-B4","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1742-6405-7-41","article-title":"Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism","volume":"7","author":"Dybowski","year":"2010","journal-title":"AIDS Res. Ther."},{"key":"2023012711591830000_btu535-B5","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","article-title":"An improved algorithm for matching biological sequences","volume":"162","author":"Gotoh","year":"1982","journal-title":"J. Mol. 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Rev. Microbiol."},{"key":"2023012711591830000_btu535-B10","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1038\/nbt1371","article-title":"Bioinformatics prediction of HIV coreceptor usage","volume":"25","author":"Lengauer","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023012711591830000_btu535-B11","doi-asserted-by":"crossref","DOI":"10.1109\/IPDPS.2009.5160931","article-title":"An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases","author":"Ligowski","year":"2009","journal-title":"Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing"},{"key":"2023012711591830000_btu535-B12","doi-asserted-by":"crossref","first-page":"251364","DOI":"10.1155\/2012\/251364","article-title":"Comparison of next-generation sequencing systems","volume":"2012","author":"Liu","year":"2012","journal-title":"J. Biomed. 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