QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors
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Mendeley | Further Information

{"title"=>"QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors", "type"=>"journal", "authors"=>[{"first_name"=>"Adam", "last_name"=>"Gudyś"}, {"first_name"=>"Sebastian", "last_name"=>"Deorowicz"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0088901", "pmid"=>"24586435"}, "id"=>"9753911e-8477-3ecf-a2c4-56a70fda5d56", "abstract"=>"Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.", "link"=>"http://www.mendeley.com/research/quickprobsa-fast-multiple-sequence-alignment-algorithm-designed-graphics-processors", "reader_count"=>13, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>4, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/1397621"], "description"=>"<p>Times are given in format.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model", "real-life", "datasets", "pfam"], "article_id"=>943844, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t011", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_results_for_the_real_life_datasets_from_Pfam_database_/943844", "title"=>"Detailed results for the real-life datasets from Pfam database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397622"], "description"=>"<p>Speed-ups of QuickProbs (CPU+GPU) over MSAProbs (CPU) across different hardware configurations are also shown.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model", "times", "oxbench-x", "benchmark"], "article_id"=>943845, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t010", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Execution_times_for_OXBench_X_benchmark_reported_in_format_/943845", "title"=>"Execution times for OXBench-X benchmark reported in format.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397623"], "description"=>"<p>Pseudo-code of the posterior matrix calculation procedure. Statements show only general form of data dependencies. Procedure requires execution of 6 anti-diagonal passes (lines 2, , 5, 6, 7, and ). is computed first due to greater memory requirements.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model"], "article_id"=>943846, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t001", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithm_1_/943846", "title"=>"Algorithm 1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397624"], "description"=>"<p>Pseudo-code of the generalised dynamic programming forward and reversed passes. and indicate 'th row and 'th column of matrix.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model"], "article_id"=>943847, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t002", "stats"=>{"downloads"=>9, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithm_2_/943847", "title"=>"Algorithm 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397625"], "description"=>"<p>Pseudo-code of the sparse matrix generation procedure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model"], "article_id"=>943848, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t003", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithm_3_/943848", "title"=>"Algorithm 3.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397626"], "description"=>"<p>Pseudo-code of the posterior matrix relaxation procedure.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model"], "article_id"=>943849, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithm_4_/943849", "title"=>"Algorithm 4.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397627"], "description"=>"<p>Top three rows describe the CPUs. The bottom four rows describe the GPUs.</p>1<p>CPUs are equipped with HT technology. Table gives the number of physical cores.</p>2<p>On GeForce GPUs each compute unit posses 64 KB memory shared by L1 cache and local memory configured by default in ratio 16/48.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model"], "article_id"=>943850, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t005", "stats"=>{"downloads"=>6, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_hardware_used_in_the_experiments_/943850", "title"=>"Characteristics of hardware used in the experiments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397628"], "description"=>"<p>A single set of sequences is described by the number of sequences and the average sequence length .</p><p>Table presents means and standard deviations of these parameters for BAliBASE 3.0, PREFAB 4.0, and OXBench-X.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model", "amino-acid", "benchmarks"], "article_id"=>943851, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t006", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_amino_acid_benchmarks_used_in_experiments_/943851", "title"=>"Characteristics of amino-acid benchmarks used in experiments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397629"], "description"=>"<p>Each set is described by the number of sequences and the average sequence length .</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model", "taken", "pfam"], "article_id"=>943852, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901.t007", "stats"=>{"downloads"=>7, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_characteristics_of_the_protein_families_taken_from_Pfam_database_/943852", "title"=>"Detailed characteristics of the protein families taken from Pfam database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1397630"], "description"=>"<div><p>Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Genome sequencing", "Sequence analysis", "proteomics", "algorithms", "Computer applications", "Computer-aided design", "Computer architecture", "Computer hardware", "Computer modeling", "Computing methods", "Computer graphics", "Mathematical computing", "Programming languages", "software engineering", "Computer benchmarking", "Human factors engineering", "Man computer interface", "Probability theory", "Markov model", "alignment", "algorithm", "designed", "graphics"], "article_id"=>943853, "categories"=>["Biological Sciences", "Mathematics", "Engineering"], "users"=>["Adam Gudyś", "Sebastian Deorowicz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0088901", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QuickProbs_8212_A_Fast_Multiple_Sequence_Alignment_Algorithm_Designed_for_Graphics_Processors_/943853", "title"=>"QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-25 02:59:58"}

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Relative Metric

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