{"id":"https://openalex.org/W1989176519","doi":"https://doi.org/10.1186/s12859-014-0442-7","title":"MDAT- Aligning multiple domain arrangements","display_name":"MDAT- Aligning multiple domain arrangements","publication_year":2015,"publication_date":"2015-01-27","ids":{"openalex":"https://openalex.org/W1989176519","doi":"https://doi.org/10.1186/s12859-014-0442-7","mag":"1989176519","pmid":"https://pubmed.ncbi.nlm.nih.gov/25626688"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-014-0442-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0442-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0442-7","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/counter/pdf/10.1186/s12859-014-0442-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"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  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  M\u00fcnster Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"middle","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":false,"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  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  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  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  M\u00fcnster Germany","institution_ids":["https://openalex.org/I22465464"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5075543102"],"corresponding_institution_ids":["https://openalex.org/I22465464"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2058,"currency":"EUR","value_usd":2219},"fwci":0.2754,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.5846772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7278000116348267,"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":0.7278000116348267,"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":0.04969999939203262,"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/T11162","display_name":"Enzyme Structure and Function","score":0.03819999843835831,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.535637617111206},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5325977206230164},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5285355448722839},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4948510527610779},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36378705501556396},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20169082283973694},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0984392762184143},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09405592083930969},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08417841792106628}],"concepts":[{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.535637617111206},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5325977206230164},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5285355448722839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4948510527610779},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36378705501556396},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20169082283973694},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0984392762184143},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09405592083930969},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08417841792106628},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-014-0442-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0442-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0442-7","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:25626688","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25626688","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:3349782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4384290","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:a9e90d03-dda8-42c5-a6fd-6d2c30fd4829","is_oa":true,"landing_page_url":"https://miami.uni-muenster.de/Record/a9e90d03-dda8-42c5-a6fd-6d2c30fd4829","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/s12859-014-0442-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0442-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0442-7","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":[],"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/W1989176519.pdf","grobid_xml":"https://content.openalex.org/works/W1989176519.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W80140380","https://openalex.org/W1977516605","https://openalex.org/W1986347357","https://openalex.org/W1990056477","https://openalex.org/W2029582065","https://openalex.org/W2045839655","https://openalex.org/W2066694823","https://openalex.org/W2080764633","https://openalex.org/W2092003722","https://openalex.org/W2094031081","https://openalex.org/W2096745364","https://openalex.org/W2101418959","https://openalex.org/W2102502076","https://openalex.org/W2127322768","https://openalex.org/W2127774597","https://openalex.org/W2130581715","https://openalex.org/W2133793243","https://openalex.org/W2134025725","https://openalex.org/W2134063387","https://openalex.org/W2136280642","https://openalex.org/W2136570298","https://openalex.org/W2138122982","https://openalex.org/W2141885858","https://openalex.org/W2143210482","https://openalex.org/W2144362290","https://openalex.org/W2145155821","https://openalex.org/W2145268834","https://openalex.org/W2156372459","https://openalex.org/W2162800127","https://openalex.org/W2170702273","https://openalex.org/W4210323379","https://openalex.org/W4320301318","https://openalex.org/W6681765588"],"related_works":["https://openalex.org/W2748952813","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/W1971568933","https://openalex.org/W2013243191"],"abstract_inverted_index":{"BACKGROUND:":[0],"Proteins":[1],"are":[2,31],"composed":[3],"of":[4,14,26,43,50,75,125],"domains,":[5],"protein":[6,16,114],"segments":[7],"that":[8],"fold":[9],"independently":[10],"from":[11],"the":[12,15,24,41,48,90,123,136],"rest":[13],"and":[17,88,112,116,127,135],"have":[18],"a":[19,80,94],"specific":[20],"function.":[21],"During":[22],"evolution":[23,124],"arrangement":[25],"domains":[27,30],"can":[28],"change:":[29],"gained,":[32],"lost":[33],"or":[34],"their":[35,128],"order":[36],"is":[37,131,139],"rearranged.":[38],"To":[39],"facilitate":[40],"analysis":[42],"these":[44],"changes":[45,107],"we":[46],"propose":[47],"use":[49],"multiple":[51,64],"domain":[52,65,76,81,86,91,109],"alignments.":[53],"RESULTS:":[54],"We":[55],"developed":[56],"an":[57],"alignment":[58,98],"program,":[59],"called":[60],"MDAT,":[61],"which":[62,71],"aligns":[63,89],"arrangements.":[66,77],"MDAT":[67,78,101,130],"extends":[68],"earlier":[69],"programs":[70],"perform":[72],"pairwise":[73],"alignments":[74],"uses":[79],"similarity":[82],"matrix":[83],"to":[84],"score":[85],"pairs":[87],"arrangements":[92,110],"using":[93],"consistency":[95],"supported":[96],"progressive":[97],"method.":[99],"CONCLUSION:":[100],"will":[102,117],"be":[103],"useful":[104],"for":[105,142],"analysing":[106],"in":[108,133],"within":[111],"between":[113],"families":[115],"thus":[118],"provide":[119],"valuable":[120],"insights":[121],"into":[122],"proteins":[126],"domains.":[129],"coded":[132],"C++,":[134],"source":[137],"code":[138],"freely":[140],"available":[141],"download":[143],"at":[144],"http://www.bornberglab.org/pages/mdat":[145],".":[146]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
