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While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a\n                      <jats:inline-formula>\n                        <jats:alternatives>\n                          <jats:tex-math>$$\\sim$$<\/jats:tex-math>\n                          <mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                            <mml:mo>\u223c<\/mml:mo>\n                          <\/mml:math>\n                        <\/jats:alternatives>\n                      <\/jats:inline-formula>\n                      \u00a0$3000 Xilinx Alveo U50 FPGA accelerator card,\n                      <jats:inline-formula>\n                        <jats:alternatives>\n                          <jats:tex-math>$$\\sim$$<\/jats:tex-math>\n                          <mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                            <mml:mo>\u223c<\/mml:mo>\n                          <\/mml:math>\n                        <\/jats:alternatives>\n                      <\/jats:inline-formula>\n                      \u00a0227\u00d7 faster than the optimized SSV implementation in\n                      <jats:italic>nhmmer<\/jats:italic>\n                      . Accounting for PCI-e data transfer data processing, HAVAC is 65\u00d7 faster than nhmmer\u2019s SSV with one thread and 35\u00d7 faster than nhmmer with four threads, and uses\n                      <jats:inline-formula>\n                        <jats:alternatives>\n                          <jats:tex-math>$$\\sim$$<\/jats:tex-math>\n                          <mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                            <mml:mo>\u223c<\/mml:mo>\n                          <\/mml:math>\n                        <\/jats:alternatives>\n                      <\/jats:inline-formula>\n                      \u00a031% the energy of a traditional high end Intel CPU.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-024-05879-3","type":"journal-article","created":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T08:54:48Z","timestamp":1722243288000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models"],"prefix":"10.1186","volume":"25","author":[{"given":"Tim","family":"Anderson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Travis J.","family":"Wheeler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,29]]},"reference":[{"issue":"1","key":"5879_CR1","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1186\/s13059-023-02972-3","volume":"24","author":"K Sahlin","year":"2023","unstructured":"Sahlin K, Baudeau T, Cazaux B, Marchet C. 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