{"id":"https://openalex.org/W7164006136","doi":"https://doi.org/10.1186/s12859-026-06506-z","title":"LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference","display_name":"LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference","publication_year":2026,"publication_date":"2026-06-09","ids":{"openalex":"https://openalex.org/W7164006136","doi":"https://doi.org/10.1186/s12859-026-06506-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/42265603"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06506-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06506-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://doi.org/10.1186/s12859-026-06506-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138243673","display_name":"Yu Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Zhao","raw_affiliation_strings":["Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138215172","display_name":"Yi-Fei Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi-Fei Lu","raw_affiliation_strings":["Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134752884","display_name":"Xuan Hai","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuan Hai","raw_affiliation_strings":["Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101991765","display_name":"Xiao\u2010Yang Zhi","orcid":"https://orcid.org/0000-0002-9862-377X"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiao-Yang Zhi","raw_affiliation_strings":["Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China. xyzhi@ynu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yunnan Institute of Microbiology, Key Laboratory of Microbial Diversity in Southwest China of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, People's Republic of China. xyzhi@ynu.edu.cn","institution_ids":["https://openalex.org/I189210763"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101991765"],"corresponding_institution_ids":["https://openalex.org/I189210763"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.52077199,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4733000099658966,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4733000099658966,"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":0.27149999141693115,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.1800999939441681,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/inference","display_name":"Inference","score":0.7027000188827515},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.616100013256073},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5478000044822693},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.48919999599456787},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48420000076293945},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4805000126361847},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.46160000562667847},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.4603999853134155},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4244000017642975},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4171999990940094}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7027000188827515},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.616100013256073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5996999740600586},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5478000044822693},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5264000296592712},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.48919999599456787},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48420000076293945},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4805000126361847},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.46160000562667847},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4603999853134155},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4244000017642975},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4171999990940094},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.413100004196167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39719998836517334},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.39590001106262207},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3901999890804291},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38580000400543213},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.36660000681877136},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.3537999987602234},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.35019999742507935},{"id":"https://openalex.org/C39238701","wikidata":"https://www.wikidata.org/wiki/Q2091816","display_name":"Computational genomics","level":5,"score":0.34880000352859497},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.3452000021934509},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.3361999988555908},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.33390000462532043},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.3260999917984009},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.3172000050544739},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.31310001015663147},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.28870001435279846},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.28850001096725464},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.2874999940395355},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.2874000072479248},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.2842000126838684},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.27959999442100525},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26910001039505005},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.26589998602867126},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.2614000141620636},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2603999972343445},{"id":"https://openalex.org/C2909108991","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Orthologous Gene","level":4,"score":0.26019999384880066},{"id":"https://openalex.org/C2984324147","wikidata":"https://www.wikidata.org/wiki/Q3080021","display_name":"Gene selection","level":5,"score":0.25529998540878296},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2522999942302704}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering 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":"D000465","descriptor_name":"Algorithms","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-026-06506-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06506-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42265603","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42265603","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:13474896","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13474896/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13474896/pdf/12859_2026_Article_6506.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ca317b1e76434bf3b75db55a9c77aa73","is_oa":false,"landing_page_url":"https://doaj.org/article/ca317b1e76434bf3b75db55a9c77aa73","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 27, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06506-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06506-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5051236510","display_name":"\u9ad8\u6e29\u653e\u7ebf\u83cc\u57fa\u56e0\u7ec4\u7cfb\u7edf\u53d1\u80b2\u4e0e\u6e29\u5ea6\u9002\u5e94\u8fdb\u5316\u673a\u5236\u7814\u7a76","funder_award_id":"32060003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324731","display_name":"Yunnan University","ror":"https://ror.org/0040axw97"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W2002850151","https://openalex.org/W2008856488","https://openalex.org/W2019009079","https://openalex.org/W2096093282","https://openalex.org/W2099321785","https://openalex.org/W2122673596","https://openalex.org/W2128366083","https://openalex.org/W2131232002","https://openalex.org/W2138122982","https://openalex.org/W2897249806","https://openalex.org/W2951149542","https://openalex.org/W2969371653","https://openalex.org/W2988396470","https://openalex.org/W3025857586","https://openalex.org/W3045244624","https://openalex.org/W3143063265","https://openalex.org/W4235169531","https://openalex.org/W4400987661","https://openalex.org/W4401367327","https://openalex.org/W4416092382"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Orthologous":[1],"gene":[2,28,189],"inference":[3,151],"is":[4,36,173],"a":[5,21,48,124],"crucial":[6],"technical":[7],"challenge":[8],"in":[9,85,170],"evolutionary":[10],"biology.":[11],"It":[12,133],"typically":[13],"depends":[14],"on":[15,54,95],"sequence":[16,33],"similarity":[17,34,56],"searches":[18],"and":[19,61,101,115,130,148],"employs":[20],"graph":[22,64],"clustering":[23,65,93],"method":[24,49],"to":[25,70,160],"infer":[26],"homologous":[27,188],"families.":[29],"However,":[30],"the":[31,55,86,161],"all-vs-all":[32],"search":[35],"time-consuming":[37],"for":[38,176],"large-scale":[39],"genome":[40],"datasets.":[41],"In":[42],"this":[43],"work,":[44],"we":[45],"present":[46],"LSGFA,":[47],"that":[50,72,121],"detects":[51],"subgraphs":[52],"based":[53,94],"of":[57,76,103,164],"protein":[58,77,89],"domain":[59,90,97,168],"architectures":[60,169],"then":[62],"performs":[63],"within":[66],"each":[67],"subgraph,":[68],"corresponding":[69],"sequences":[71],"share":[73],"similar":[74],"compositions":[75],"domains.":[78],"RESULTS:":[79],"LSGFA":[80,122,172],"carries":[81],"out":[82],"four":[83],"steps":[84],"analysis":[87],"workflow:":[88],"annotation,":[91],"initial":[92],"Pfam":[96],"architecture,":[98],"SSN-based":[99],"clustering,":[100],"detection":[102],"pan-genomic":[104],"patterns.":[105],"Benchmarking":[106],"against":[107],"five":[108],"state-of-the-art":[109],"tools":[110],"(OrthoFinder,":[111],"Roary,":[112],"PanTA,":[113],"Panaroo,":[114],"PGAP2)":[116],"across":[117],"multiple":[118],"datasets":[119],"demonstrates":[120],"achieves":[123],"balanced":[125],"trade-off":[126],"between":[127],"computational":[128,183],"efficiency":[129],"biological":[131],"accuracy.":[132],"takes":[134],"less":[135],"time":[136,184],"than":[137,144],"OrthoFinder":[138],"while":[139,185],"identifying":[140],"more":[141],"core":[142],"genes":[143],"high-speed":[145],"heuristic":[146],"tools,":[147],"its":[149],"orthogroup":[150],"results":[152],"show":[153],"strong":[154],"consistency":[155],"with":[156,166],"OrthoFinder.":[157],"CONCLUSIONS:":[158],"Due":[159],"high":[162],"proportion":[163],"proteins":[165],"known":[167],"prokaryotes,":[171],"particularly":[174],"well-suited":[175],"prokaryotic":[177],"genomes,":[178],"where":[179],"it":[180],"significantly":[181],"reduces":[182],"yielding":[186],"accurate":[187],"inference.":[190]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-10T00:00:00"}
