{"id":"https://openalex.org/W2972411752","doi":"https://doi.org/10.1186/s12859-019-3019-7","title":"HH-suite3 for fast remote homology detection and deep protein annotation","display_name":"HH-suite3 for fast remote homology detection and deep protein annotation","publication_year":2019,"publication_date":"2019-09-14","ids":{"openalex":"https://openalex.org/W2972411752","doi":"https://doi.org/10.1186/s12859-019-3019-7","mag":"2972411752","pmid":"https://pubmed.ncbi.nlm.nih.gov/31521110"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3019-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3019-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3019-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3019-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019985343","display_name":"Martin Steinegger","orcid":"https://orcid.org/0000-0001-8781-9753"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Martin Steinegger","raw_affiliation_strings":["Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA","Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]},{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051877041","display_name":"Markus Meier","orcid":"https://orcid.org/0000-0003-1068-746X"},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Meier","raw_affiliation_strings":["Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016012053","display_name":"Milot Mirdita","orcid":"https://orcid.org/0000-0001-8637-6719"},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Milot Mirdita","raw_affiliation_strings":["Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022607933","display_name":"Harald V\u00f6hringer","orcid":"https://orcid.org/0000-0003-2513-4518"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]},{"id":"https://openalex.org/I4210137637","display_name":"Bioinformatics Institute","ror":"https://ror.org/04btxg914","country_code":"RU","type":"nonprofit","lineage":["https://openalex.org/I4210137637"]}],"countries":["DE","GB","RU"],"is_corresponding":false,"raw_author_name":"Harald V\u00f6hringer","raw_affiliation_strings":["European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom","Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I4210137637"]},{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060145781","display_name":"Stephan J. Haunsberger","orcid":null},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Stephan J. Haunsberger","raw_affiliation_strings":["Royal College of Surgeons, Dublin, D02 YN77, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Royal College of Surgeons, Dublin, D02 YN77, Ireland","institution_ids":["https://openalex.org/I142762351"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010030898","display_name":"Johannes S\u00f6ding","orcid":"https://orcid.org/0000-0001-9642-8244"},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johannes S\u00f6ding","raw_affiliation_strings":["Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany. soeding@mpibpc.mpg.de","Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9642-8244","affiliations":[{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany. soeding@mpibpc.mpg.de","institution_ids":["https://openalex.org/I4210131661"]},{"raw_affiliation_string":"Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Munich, 81379, Germany","institution_ids":["https://openalex.org/I4210131661"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010030898"],"corresponding_institution_ids":["https://openalex.org/I4210131661"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":38.6084,"has_fulltext":true,"cited_by_count":1300,"citation_normalized_percentile":{"value":0.99908523,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"473","last_page":"473"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.37560001015663147,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.37560001015663147,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.15760000050067902,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.12809999287128448,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8073440790176392},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.6913321018218994},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.6790839433670044},{"id":"https://openalex.org/keywords/viterbi-algorithm","display_name":"Viterbi algorithm","score":0.605536162853241},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5429763793945312},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.513659656047821},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5110929608345032},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4975176155567169},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.48626744747161865},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.48567521572113037},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.44380876421928406},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4249618947505951},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.41248810291290283},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3411245048046112},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3339918255805969},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.200095534324646},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.18217802047729492},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14169806241989136},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14029642939567566}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8073440790176392},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6913321018218994},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.6790839433670044},{"id":"https://openalex.org/C60582962","wikidata":"https://www.wikidata.org/wiki/Q83886","display_name":"Viterbi algorithm","level":3,"score":0.605536162853241},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5429763793945312},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.513659656047821},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5110929608345032},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4975176155567169},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.48626744747161865},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.48567521572113037},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.44380876421928406},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4249618947505951},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.41248810291290283},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3411245048046112},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3339918255805969},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.200095534324646},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.18217802047729492},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14169806241989136},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14029642939567566},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-3019-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3019-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3019-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31521110","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31521110","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6744700","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6744700","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:59e6cde7518149c596f2e8cd8b7e6c97","is_oa":false,"landing_page_url":"https://doaj.org/article/59e6cde7518149c596f2e8cd8b7e6c97","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-15 (2019)","raw_type":"article"},{"id":"pmh:oai:publications.goettingen-research-online.de:2/102891","is_oa":true,"landing_page_url":"https://resolver.sub.uni-goettingen.de/purl?gro-2/102891","pdf_url":null,"source":{"id":"https://openalex.org/S4306401634","display_name":"GoeScholar  The Publication Server of the Georg-August-Universit\u00e4t G\u00f6ttingen (Georg-August-Universit\u00e4t G\u00f6ttingen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210122495","host_organization_name":"Asklepios Klinik St. Georg","host_organization_lineage":["https://openalex.org/I4210122495"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal_article"},{"id":"pmh:oai:s-space.snu.ac.kr:10371/202569","is_oa":false,"landing_page_url":"https://hdl.handle.net/10371/202569","pdf_url":null,"source":{"id":"https://openalex.org/S4306401345","display_name":"Seoul National University Open Repository (Seoul National University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139264467","host_organization_name":"Seoul National University","host_organization_lineage":["https://openalex.org/I139264467"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3019-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3019-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3019-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G1653626626","display_name":null,"funder_award_id":"685778","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"},{"id":"https://openalex.org/G4671512033","display_name":null,"funder_award_id":"685778","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320310016","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993"},{"id":"https://openalex.org/F4320332431","display_name":"College of Engineering, Michigan State University","ror":"https://ror.org/05hs6h993"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2972411752.pdf","grobid_xml":"https://content.openalex.org/works/W2972411752.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2006899413","https://openalex.org/W2008708467","https://openalex.org/W2011652244","https://openalex.org/W2014050554","https://openalex.org/W2015530520","https://openalex.org/W2015915218","https://openalex.org/W2045204781","https://openalex.org/W2051210555","https://openalex.org/W2062693912","https://openalex.org/W2102124048","https://openalex.org/W2105961968","https://openalex.org/W2124351063","https://openalex.org/W2128653811","https://openalex.org/W2130479394","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2133540884","https://openalex.org/W2137597742","https://openalex.org/W2138122982","https://openalex.org/W2145268834","https://openalex.org/W2145541064","https://openalex.org/W2146379626","https://openalex.org/W2147667050","https://openalex.org/W2149525061","https://openalex.org/W2150853465","https://openalex.org/W2151831732","https://openalex.org/W2158714788","https://openalex.org/W2159591897","https://openalex.org/W2162758337","https://openalex.org/W2166081493","https://openalex.org/W2511687775","https://openalex.org/W2557595285","https://openalex.org/W2563361853","https://openalex.org/W2898402099","https://openalex.org/W2900359059","https://openalex.org/W2950954328","https://openalex.org/W3145289798"],"related_works":["https://openalex.org/W2948014085","https://openalex.org/W1741740882","https://openalex.org/W2103737249","https://openalex.org/W2004215917","https://openalex.org/W2143450062","https://openalex.org/W2620591814","https://openalex.org/W2014072682","https://openalex.org/W1486249959","https://openalex.org/W2005647400","https://openalex.org/W24291664"],"abstract_inverted_index":{"BACKGROUND:":[0],"HH-suite":[1],"is":[2,20,83,126],"a":[3,42,68,74],"widely":[4],"used":[5],"open":[6],"source":[7],"software":[8,125],"suite":[9],"for":[10,52],"sensitive":[11],"sequence":[12,34],"similarity":[13],"searches":[14,99],"and":[15,56,71,88,97,110,116,135,140,150,156],"protein":[16,148],"fold":[17],"recognition.":[18],"It":[19],"based":[21],"on":[22],"pairwise":[23],"alignment":[24,55],"of":[25,36,48,138],"profile":[26,53,103],"Hidden":[27],"Markov":[28],"models":[29],"(HMMs),":[30],"which":[31],"represent":[32],"multiple":[33],"alignments":[35],"homologous":[37],"proteins.":[38],"RESULTS:":[39],"We":[40],"developed":[41],"single-instruction":[43],"multiple-data":[44],"(SIMD)":[45],"vectorized":[46],"implementation":[47],"the":[49,63,78],"Viterbi":[50],"algorithm":[51],"HMM":[54],"introduced":[57],"various":[58],"other":[59],"speed-ups.":[60],"These":[61],"accelerated":[62],"search":[64],"methods":[65],"HHsearch":[66,96,139],"by":[67,73],"factor":[69,75],"4":[70],"HHblits":[72,98,141],"2":[76],"over":[77,108,111],"previous":[79],"version":[80],"2.0.16.":[81],"HHblits3":[82],"\u223c10\u00d7":[84],"faster":[85,90],"than":[86,91],"PSI-BLAST":[87],"\u223c20\u00d7":[89],"HMMER3.":[92],"Jobs":[93],"to":[94],"perform":[95],"with":[100],"many":[101],"query":[102],"HMMs":[104],"can":[105],"be":[106],"parallelized":[107],"cores":[109],"cluster":[112],"servers":[113],"using":[114],"OpenMP":[115],"message":[117],"passing":[118],"interface":[119],"(MPI).":[120],"The":[121,132],"free,":[122],"open-source,":[123],"GPLv3-licensed":[124],"available":[127],"at":[128],"https://github.com/soedinglab/hh-suite":[129],".":[130],"CONCLUSION:":[131],"added":[133],"functionalities":[134],"increased":[136],"speed":[137],"should":[142],"facilitate":[143],"their":[144],"use":[145],"in":[146,154],"large-scale":[147],"structure":[149],"function":[151],"prediction,":[152],"e.g.":[153],"metagenomics":[155],"genomics":[157],"projects.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":86},{"year":2025,"cited_by_count":185},{"year":2024,"cited_by_count":253},{"year":2023,"cited_by_count":289},{"year":2022,"cited_by_count":195},{"year":2021,"cited_by_count":208},{"year":2020,"cited_by_count":73},{"year":2019,"cited_by_count":10},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}