{"id":"https://openalex.org/W1485087568","doi":"https://doi.org/10.1186/s12859-015-0570-8","title":"Domain similarity based orthology detection","display_name":"Domain similarity based orthology detection","publication_year":2015,"publication_date":"2015-05-12","ids":{"openalex":"https://openalex.org/W1485087568","doi":"https://doi.org/10.1186/s12859-015-0570-8","mag":"1485087568","pmid":"https://pubmed.ncbi.nlm.nih.gov/25968113"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0570-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0570-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0570-8","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/counter/pdf/10.1186/s12859-015-0570-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006821640","display_name":"Tristan Bitard\u2010Feildel","orcid":"https://orcid.org/0000-0001-7550-560X"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Tristan Bitard-Feildel","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. t.bitard.feildel@uni-muenster.de","Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. t.bitard.feildel@uni-muenster.de","institution_ids":["https://openalex.org/I22465464"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075543102","display_name":"Carsten Kemena","orcid":"https://orcid.org/0000-0002-2416-9842"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Carsten Kemena","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. c.kemena@uni-muenster.de","Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. c.kemena@uni-muenster.de","institution_ids":["https://openalex.org/I22465464"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006664933","display_name":"Jenny M. Greenwood","orcid":null},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]},{"id":"https://openalex.org/I4210103666","display_name":"University Hospital M\u00fcnster","ror":"https://ror.org/01856cw59","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210103666"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jenny M Greenwood","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. j.greenwood@uni-muenster.de","Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. j.greenwood@uni-muenster.de","institution_ids":["https://openalex.org/I22465464","https://openalex.org/I4210096541","https://openalex.org/I4210103666"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072841736","display_name":"Erich Bornberg\u2010Bauer","orcid":"https://orcid.org/0000-0002-1826-3576"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]},{"id":"https://openalex.org/I4210096541","display_name":"Institute for Biodiversity","ror":"https://ror.org/01n8ggb71","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I4210096541"]},{"id":"https://openalex.org/I4210103666","display_name":"University Hospital M\u00fcnster","ror":"https://ror.org/01856cw59","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210103666"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erich Bornberg-Bauer","raw_affiliation_strings":["Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. ebb@uni-muenster.de","Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany. ebb@uni-muenster.de","institution_ids":["https://openalex.org/I22465464","https://openalex.org/I4210096541","https://openalex.org/I4210103666"]},{"raw_affiliation_string":"Institute for Evolution and Biodiversity, University of M\u00fcnster, H\u00fcfferstr. 1, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006821640"],"corresponding_institution_ids":["https://openalex.org/I22465464"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":865,"currency":"EUR","value_usd":932},"fwci":0.6886,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.68257612,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"1","first_page":"154","last_page":"154"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.736299991607666,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.736299991607666,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.07639999687671661,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06319999694824219,"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/dna-microarray","display_name":"DNA microarray","score":0.61890709400177},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6163032054901123},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6074562072753906},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5681703686714172},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49369463324546814},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4800221025943756},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2820577025413513},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2782139182090759},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19194594025611877},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1263202726840973},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.124163419008255}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.61890709400177},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6163032054901123},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6074562072753906},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5681703686714172},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49369463324546814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4800221025943756},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2820577025413513},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2782139182090759},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19194594025611877},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1263202726840973},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.124163419008255},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0570-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0570-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0570-8","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:25968113","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25968113","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":null},{"id":"pmh:oai:europepmc.org:3406172","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4443542","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:wwu.de:1c776766-d1a6-4fcc-8af8-c6f364a92d5c","is_oa":true,"landing_page_url":"https://nbn-resolving.org/urn:nbn:de:hbz:6-99229524256","pdf_url":null,"source":{"id":"https://openalex.org/S4306402051","display_name":"URN:NBN Resolver for Germany & Switzerland (German National Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2802635041","host_organization_name":"Technische Informationsbibliothek (TIB)","host_organization_lineage":["https://openalex.org/I2802635041"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0570-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0570-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0570-8","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1485087568.pdf","grobid_xml":"https://content.openalex.org/works/W1485087568.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1973470270","https://openalex.org/W1977516605","https://openalex.org/W1979835060","https://openalex.org/W1986347357","https://openalex.org/W1990056477","https://openalex.org/W1996423252","https://openalex.org/W1997272729","https://openalex.org/W2008856488","https://openalex.org/W2016685368","https://openalex.org/W2029833898","https://openalex.org/W2030317329","https://openalex.org/W2036696353","https://openalex.org/W2040184829","https://openalex.org/W2043092219","https://openalex.org/W2045839655","https://openalex.org/W2053913299","https://openalex.org/W2065127848","https://openalex.org/W2066694823","https://openalex.org/W2069323107","https://openalex.org/W2070987430","https://openalex.org/W2080090262","https://openalex.org/W2096745364","https://openalex.org/W2101234009","https://openalex.org/W2114676910","https://openalex.org/W2121013757","https://openalex.org/W2123775947","https://openalex.org/W2133022970","https://openalex.org/W2138122982","https://openalex.org/W2138459937","https://openalex.org/W2141885858","https://openalex.org/W2145155821","https://openalex.org/W2145268834","https://openalex.org/W2151603408","https://openalex.org/W2153562609","https://openalex.org/W2158714788","https://openalex.org/W2159455600","https://openalex.org/W2161033884","https://openalex.org/W2161394740","https://openalex.org/W4320301318","https://openalex.org/W6658033436","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2327130486"],"abstract_inverted_index":{"BACKGROUND:":[0],"Orthologous":[1],"protein":[2,99],"detection":[3,81,242],"software":[4],"mostly":[5],"uses":[6],"pairwise":[7],"comparisons":[8,33,66],"of":[9,25,32,44,55,65,73,82,88,122,170,187,193,201,216,223,231,238,247,254],"amino-acid":[10],"sequences":[11,26],"to":[12,34,60,77,90,146,175,250],"assert":[13],"whether":[14],"two":[15,97],"proteins":[16,84,149,177,213],"are":[17,132,144],"orthologous":[18,83],"or":[19],"not.":[20],"Accordingly,":[21,153],"when":[22,48],"the":[23,30,52,80,92,123,126,154,162,191,194,198,236,267],"number":[24,31,54,64],"for":[27,165,181],"comparison":[28],"increases,":[29],"compute":[35],"grows":[36],"in":[37,69],"a":[38,70,102,105,221,228,245],"quadratic":[39],"order.":[40],"A":[41],"current":[42],"challenge":[43],"bioinformatic":[45],"research,":[46],"especially":[47],"taking":[49],"into":[50,150],"account":[51],"increasing":[53],"sequenced":[56],"organisms":[57],"available,":[58],"is":[59,158,256,264],"make":[61],"this":[62],"ever-growing":[63],"computationally":[67],"feasible":[68],"reasonable":[71],"amount":[72],"time.":[74],"We":[75,95,207],"propose":[76],"speed":[78],"up":[79,240],"by":[85],"using":[86,184,258],"strings":[87,215],"domains":[89,185],"characterize":[91],"proteins.":[93],"RESULTS:":[94],"present":[96],"new":[98,116],"similarity":[100,130,156,173],"measures,":[101],"cosine":[103,124,155],"and":[104,115,125,211,260,263],"maximal":[106,127],"weight":[107,128],"matching":[108,129],"score":[109],"based":[110],"on":[111],"domain":[112,141,171],"content":[113,142,172],"similarity,":[114],"software,":[117],"named":[118],"porthoDom.":[119],"The":[120,137,252],"qualities":[121],"measures":[131,138,174],"compared":[133],"against":[134],"curated":[135],"datasets.":[136],"show":[139],"that":[140,209],"similarities":[143],"able":[145],"correctly":[147],"group":[148,176],"their":[151,224],"families.":[152],"measure":[157],"used":[159],"inside":[160],"porthoDom,":[161],"wrapper":[163],"developed":[164],"proteinortho.":[166,251],"porthoDom":[167,234,255],"makes":[168],"use":[169],"together":[178],"before":[179],"searching":[180],"orthologs.":[182],"By":[183],"instead":[186],"amino":[188],"acid":[189],"sequences,":[190],"reduction":[192],"search":[195,232],"space":[196],"decreases":[197],"computational":[199],"complexity":[200],"an":[202],"all-against-all":[203],"sequence":[204],"comparison.":[205],"CONCLUSION:":[206],"demonstrate":[208],"representing":[210],"comparing":[212],"as":[214,220],"discrete":[217],"domains,":[218],"i.e.":[219],"concatenation":[222],"unique":[225],"identifiers,":[226],"allows":[227],"drastic":[229],"simplification":[230],"space.":[233],"has":[235],"advantage":[237],"speeding":[239],"orthology":[241],"while":[243],"maintaining":[244],"degree":[246],"accuracy":[248],"similar":[249],"implementation":[253],"released":[257],"python":[259],"C++":[261],"languages":[262],"available":[265],"under":[266],"GNU":[268],"GPL":[269],"licence":[270],"3":[271],"at":[272],"http://www.bornberglab.org/pages/porthoda":[273],".":[274]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
