{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T00:10:07Z","timestamp":1751587807083,"version":"3.41.0"},"reference-count":33,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"10","license":[{"start":{"date-parts":[[2018,10,1]],"date-time":"2018-10-01T00:00:00Z","timestamp":1538352000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Parallel Distrib. Syst."],"published-print":{"date-parts":[[2018,10,1]]},"DOI":"10.1109\/tpds.2018.2830393","type":"journal-article","created":{"date-parts":[[2018,4,26]],"date-time":"2018-04-26T18:55:25Z","timestamp":1524768925000},"page":"2206-2222","source":"Crossref","is-referenced-by-count":3,"title":["CUDAMPF++: A Proactive Resource Exhaustion Scheme for Accelerating Homologous Sequence Search on CUDA-Enabled GPU"],"prefix":"10.1109","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7827-0719","authenticated-orcid":false,"given":"Hanyu","family":"Jiang","sequence":"first","affiliation":[]},{"given":"Narayan","family":"Ganesan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3868-0593","authenticated-orcid":false,"given":"Yu-Dong","family":"Yao","sequence":"additional","affiliation":[]}],"member":"263","reference":[{"year":"2015","key":"ref33","article-title":"Tesla K80 GPU accelerator"},{"article-title":"Overview of amazon web services","year":"2014","author":"varia","key":"ref32"},{"year":"2018","key":"ref31"},{"key":"ref30","first-page":"24","article-title":"CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application","author":"ping","year":"2010","journal-title":"Proc Int Conf High Perform Comput Simul"},{"key":"ref10","first-page":"332","article-title":"Accelerating HMMER search using FPGA","author":"takagi","year":"2009","journal-title":"Proc Intl Conf Field Programmable Logic and Appl"},{"key":"ref11","first-page":"37","article-title":"Accelerating HMMER on FPGA using parallel prefixes and reductions","author":"abbas","year":"2010","journal-title":"Proc Int Conf Field-Programmable Technol"},{"key":"ref12","first-page":"73","article-title":"A speculative HMMER search implementation on GPU","author":"li","year":"2012","journal-title":"26th IPDPS Workshops & PhD Forum"},{"article-title":"Implementing and accelerating HMMER3 protein sequence search on CUDA-enabled GPU","year":"2014","author":"cheng","key":"ref13"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/978-3-319-18120-2_17","article-title":"Accelerating search of protein sequence databases using CUDA-enabled GPU","author":"cheng","year":"2015","journal-title":"Proc Int Conf Database Syst Adv Appl"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-165"},{"key":"ref16","first-page":"65","article-title":"Acceleration of single- and multiple-segment viterbi algorithms for biological sequence-profile comparison on GPU","author":"de arajo neto","year":"2015","journal-title":"Proc 21st Int Conf Parallel Distrib Process Techn Appl"},{"key":"ref17","first-page":"375","article-title":"Fine-grained acceleration of HMMER 3.0 via architecture-aware optimization on massively parallel processors","author":"jiang","year":"2015","journal-title":"Proc 14th IEEE Int Workshop High Perform Comput Biol"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-0946-4"},{"key":"ref19","article-title":"The SSV filter implementation","author":"bjarne","year":"2015","journal-title":"HMMER v3 1b2 Source Code"},{"article-title":"The little redis book","year":"2012","author":"karl","key":"ref28"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1006\/jmbi.1994.1104","article-title":"Hidden Markov models in computational biology: Applications to protein modeling","volume":"235","author":"anders","year":"1994","journal-title":"J Molecular Biol"},{"year":"2013","key":"ref27"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"ref6","first-page":"1","article-title":"Evaluating the use of GPUs in liver image segmentation and HMMER database searches","author":"walters","year":"2009","journal-title":"Proc Int Symp Parallel Distrib Process"},{"key":"ref29","first-page":"11","article-title":"ClawHMMER: A streaming HMMer-search implementation","author":"horn","year":"2005","journal-title":"Proc ACM\/IEEE Supercomputing Conf"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1145\/1183401.1183442","article-title":"Accelerator design for protein sequence HMM search","author":"maddimsetty","year":"2006","journal-title":"Proc 20th ACM Int'l Conf Supercomputing"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1145\/1854776.1854844"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/14.9.755"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1016\/j.parco.2008.08.003"},{"key":"ref1","first-page":"870","article-title":"Graphics processing units in bioinformatics, computational biology and systems biology","volume":"18","author":"marco s","year":"2017","journal-title":"Briefings Bioinf"},{"key":"ref20","first-page":"483","article-title":"Validity of the single-processor approach to achieving large-scale computing capabilities","author":"amdahl","year":"1967","journal-title":"Proc Sprint Joint Comput Conf Amer Fed Inf Process Societies"},{"year":"2014","key":"ref22","article-title":"NVIDIAs next generation CUDA compute architecture: Kepler GK110\/210"},{"year":"2017","key":"ref21","article-title":"CUDA C programming guide"},{"year":"2014","key":"ref24"},{"year":"2017","key":"ref23","article-title":"Parallel thread execution ISA"},{"year":"2017","key":"ref26","article-title":"Profiler user’s guide"},{"year":"2013","key":"ref25","article-title":"NVIDIA Tesla GPU accelerators"}],"container-title":["IEEE Transactions on Parallel and Distributed Systems"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/71\/8458269\/08350332.pdf?arnumber=8350332","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T23:29:39Z","timestamp":1751585379000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/8350332\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,1]]},"references-count":33,"journal-issue":{"issue":"10"},"URL":"https:\/\/doi.org\/10.1109\/tpds.2018.2830393","relation":{},"ISSN":["1045-9219","1558-2183","2161-9883"],"issn-type":[{"type":"print","value":"1045-9219"},{"type":"electronic","value":"1558-2183"},{"type":"electronic","value":"2161-9883"}],"subject":[],"published":{"date-parts":[[2018,10,1]]}}}