{"id":"https://openalex.org/W2167832495","doi":"https://doi.org/10.1186/1471-2105-7-382","title":"MultiSeq: unifying sequence and structure data for evolutionary analysis","display_name":"MultiSeq: unifying sequence and structure data for evolutionary analysis","publication_year":2006,"publication_date":"2006-08-16","ids":{"openalex":"https://openalex.org/W2167832495","doi":"https://doi.org/10.1186/1471-2105-7-382","mag":"2167832495","pmid":"https://pubmed.ncbi.nlm.nih.gov/16914055"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-382","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-382","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-382","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/10.1186/1471-2105-7-382","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003124534","display_name":"Elijah Roberts","orcid":"https://orcid.org/0000-0002-5619-8066"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elijah Roberts","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. erobert3@scs.uiuc.edu","Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. erobert3@scs.uiuc.edu","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113433307","display_name":"John Eargle","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Eargle","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062603258","display_name":"D. Wright","orcid":"https://orcid.org/0000-0003-1018-5187"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Wright","raw_affiliation_strings":["Graduate School of Library and Information Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Library and Information Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004867963","display_name":"Zaida Luthey\u2010Schulten","orcid":"https://orcid.org/0000-0001-9749-8367"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zaida Luthey-Schulten","raw_affiliation_strings":["Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004867963"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":4.4873,"has_fulltext":true,"cited_by_count":410,"citation_normalized_percentile":{"value":0.95455688,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"382","last_page":"382"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3662000000476837,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3662000000476837,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.17030000686645508,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.11129999905824661,"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":0.6051728129386902},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5166507363319397},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.514008641242981},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4683280289173126},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4660813510417938},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.45845240354537964},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.43971961736679077},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.42601141333580017},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4034178853034973},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39813515543937683},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34494537115097046},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3066416382789612},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14991089701652527}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6051728129386902},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5166507363319397},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.514008641242981},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4683280289173126},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4660813510417938},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45845240354537964},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.43971961736679077},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.42601141333580017},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4034178853034973},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39813515543937683},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34494537115097046},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3066416382789612},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14991089701652527},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-382","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-382","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-382","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:16914055","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16914055","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:europepmc.org:1341816","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1586216","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:doaj.org/article:7279712ec8604f36b887750e9ff1a65d","is_oa":false,"landing_page_url":"https://doaj.org/article/7279712ec8604f36b887750e9ff1a65d","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 7, Iss 1, p 382 (2006)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1626326","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626326","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-382","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-382","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-382","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":[{"id":"https://openalex.org/G1191631772","display_name":null,"funder_award_id":"P41 RR005969","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G222768804","display_name":null,"funder_award_id":"DE\u2010FG02\u2010","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2233353119","display_name":null,"funder_award_id":"T32 GM 008276","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3012838438","display_name":null,"funder_award_id":"PHS5 T32 GM 08276","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3930733855","display_name":null,"funder_award_id":"PHS2P41RR05969","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G5785632311","display_name":"ROLE OF HORIZONTAL GENE TRANSFER AS A CONTROL ON THE COEVOLUTION OF RIBOSOMAL PROTEINS AND THE GENETIC CODE","funder_award_id":"FG02-05ER64144","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167832495.pdf","grobid_xml":"https://content.openalex.org/works/W2167832495.grobid-xml"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W173647602","https://openalex.org/W1508885706","https://openalex.org/W1513339763","https://openalex.org/W1931294762","https://openalex.org/W1967856778","https://openalex.org/W1984882637","https://openalex.org/W1987856282","https://openalex.org/W1996307860","https://openalex.org/W1997954369","https://openalex.org/W2003122343","https://openalex.org/W2009346772","https://openalex.org/W2015403140","https://openalex.org/W2018756788","https://openalex.org/W2020944535","https://openalex.org/W2026258231","https://openalex.org/W2027707902","https://openalex.org/W2029667189","https://openalex.org/W2053671774","https://openalex.org/W2055043387","https://openalex.org/W2060035159","https://openalex.org/W2083175946","https://openalex.org/W2084367350","https://openalex.org/W2085277871","https://openalex.org/W2094406540","https://openalex.org/W2096525273","https://openalex.org/W2097382368","https://openalex.org/W2100380699","https://openalex.org/W2102424972","https://openalex.org/W2103546861","https://openalex.org/W2105355690","https://openalex.org/W2106882534","https://openalex.org/W2107594154","https://openalex.org/W2107903949","https://openalex.org/W2108067237","https://openalex.org/W2111038162","https://openalex.org/W2114520383","https://openalex.org/W2116554395","https://openalex.org/W2118321916","https://openalex.org/W2125725297","https://openalex.org/W2130479394","https://openalex.org/W2131465715","https://openalex.org/W2132629607","https://openalex.org/W2133657429","https://openalex.org/W2135304075","https://openalex.org/W2137079713","https://openalex.org/W2138645972","https://openalex.org/W2141448511","https://openalex.org/W2141920771","https://openalex.org/W2142056356","https://openalex.org/W2143733126","https://openalex.org/W2144362290","https://openalex.org/W2146058063","https://openalex.org/W2146396346","https://openalex.org/W2148047088","https://openalex.org/W2148853951","https://openalex.org/W2149429041","https://openalex.org/W2151831732","https://openalex.org/W2155843307","https://openalex.org/W2156460914","https://openalex.org/W2156492633","https://openalex.org/W2158714788","https://openalex.org/W2162906563","https://openalex.org/W2167673850","https://openalex.org/W2169267759","https://openalex.org/W2229908198","https://openalex.org/W2327525319","https://openalex.org/W3199943451","https://openalex.org/W3217097258","https://openalex.org/W4230903726","https://openalex.org/W4230932396","https://openalex.org/W4234879553","https://openalex.org/W4234887284","https://openalex.org/W4250052351","https://openalex.org/W4251079740","https://openalex.org/W4256395558","https://openalex.org/W4285719527","https://openalex.org/W4299298909"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2133116680","https://openalex.org/W2141411672","https://openalex.org/W2029514038","https://openalex.org/W1486249959","https://openalex.org/W2141530749","https://openalex.org/W2132972885","https://openalex.org/W1977143711","https://openalex.org/W2111937814","https://openalex.org/W4290667473"],"abstract_inverted_index":{"BACKGROUND:":[0],"Since":[1],"the":[2,5,9,73,138,141,146,163,174,177,199,202,218,231,235,244,255,259,271,296,325],"publication":[3],"of":[4,8,33,97,143,165,201,206,210,222,246,251,258,262,270,280],"first":[6],"draft":[7],"human":[10],"genome":[11],"in":[12,40,45,79,95,243],"2000,":[13],"bioinformatic":[14],"data":[15,49,125,139],"have":[16],"been":[17],"accumulating":[18],"at":[19],"an":[20,184],"overwhelming":[21],"pace.":[22],"Currently,":[23],"more":[24],"than":[25],"3":[26],"million":[27],"sequences":[28,237,252],"and":[29,35,46,71,87,92,99,119,123,128,173,225,233,302,304,323],"35":[30],"thousand":[31],"structures":[32],"proteins":[34,127],"nucleic":[36,129],"acids":[37],"are":[38,292],"available":[39],"public":[41],"databases.":[42],"Finding":[43],"correlations":[44],"between":[47],"these":[48,181],"to":[50,61,69,77,83,89,115,152,169,179,192,321],"answer":[51],"critical":[52],"research":[53],"questions":[54],"is":[55,134,148,160,266,276,306],"extremely":[56],"challenging.":[57],"This":[58],"problem":[59],"needs":[60],"be":[62],"approached":[63],"from":[64,230],"several":[65],"directions:":[66],"information":[67,75],"science":[68],"organize":[70],"search":[72],"data;":[74],"visualization":[76,284],"assist":[78],"recognizing":[80],"correlations;":[81],"mathematics":[82],"formulate":[84],"statistical":[85],"inferences;":[86],"biology":[88],"analyze":[90,120],"chemical":[91],"physical":[93],"properties":[94],"terms":[96],"sequence":[98,122,224],"structure":[100,124,226],"changes.":[101],"RESULTS:":[102],"Here":[103],"we":[104],"present":[105],"MultiSeq,":[106],"a":[107,189,207,247,267,282],"unified":[108],"bioinformatics":[109],"analysis":[110],"environment":[111,147],"that":[112,197,253,275],"allows":[113],"one":[114],"organize,":[116],"display,":[117],"align":[118],"both":[121],"for":[126,176,286,299],"acids.":[130],"While":[131],"special":[132],"emphasis":[133],"placed":[135],"on":[136,217,319],"analyzing":[137,287],"within":[140],"framework":[142],"evolutionary":[144,158,195,256],"biology,":[145],"also":[149],"flexible":[150],"enough":[151],"accommodate":[153],"other":[154],"usage":[155],"patterns.":[156],"The":[157,214,314],"approach":[159],"supported":[161],"by":[162,238,295],"use":[164,324],"predefined":[166],"metadata,":[167],"adherence":[168],"standard":[170],"ontological":[171],"mappings,":[172],"ability":[175],"user":[178],"adjust":[180],"classifications":[182],"using":[183],"electronic":[185],"notebook.":[186],"MultiSeq":[187,265,305,315],"contains":[188],"new":[190],"algorithm":[191],"generate":[193],"complete":[194],"profiles":[196],"represent":[198],"topology":[200],"molecular":[203,288],"phylogenetic":[204],"tree":[205],"homologous":[208,260],"group":[209,261],"distantly":[211],"related":[212],"proteins.":[213,263],"method,":[215],"based":[216],"multidimensional":[219],"QR":[220],"factorization":[221],"multiple":[223],"alignments,":[227],"removes":[228],"redundancy":[229],"alignments":[232],"orders":[234],"protein":[236],"increasing":[239],"linear":[240],"dependence,":[241],"resulting":[242],"identification":[245],"minimal":[248],"basis":[249],"set":[250],"spans":[254],"space":[257],"CONCLUSION:":[264],"major":[268],"extension":[269],"Multiple":[272],"Alignment":[273],"tool":[274],"provided":[277],"as":[278],"part":[279],"VMD,":[281],"structural":[283],"program":[285],"dynamics":[289],"simulations.":[290],"Both":[291],"freely":[293],"distributed":[294],"NIH":[297],"Resource":[298],"Macromolecular":[300],"Modeling":[301],"Bioinformatics":[303],"included":[307],"with":[308,311],"VMD":[309],"starting":[310],"version":[312],"1.8.5.":[313],"website":[316],"has":[317],"details":[318],"how":[320],"download":[322],"software:":[326],"http://www.scs.uiuc.edu/~schulten/multiseq/":[327]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":23},{"year":2019,"cited_by_count":33},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":25},{"year":2015,"cited_by_count":24},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":26},{"year":2012,"cited_by_count":23}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}