{"id":"https://openalex.org/W2148311769","doi":"https://doi.org/10.1093/nar/29.1.323","title":"BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations","display_name":"BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations","publication_year":2001,"publication_date":"2001-01-01","ids":{"openalex":"https://openalex.org/W2148311769","doi":"https://doi.org/10.1093/nar/29.1.323","mag":"2148311769","pmid":"https://pubmed.ncbi.nlm.nih.gov/11125126"},"language":"en","primary_location":{"id":"doi:10.1093/nar/29.1.323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/29.1.323","pdf_url":"https://academic.oup.com/nar/article-pdf/29/1/323/9905805/290323.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/29/1/323/9905805/290323.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077028466","display_name":"Anne Bahr","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210086872","display_name":"Institut de g\u00e9n\u00e9tique et de biologie mol\u00e9culaire et cellulaire","ror":"https://ror.org/0015ws592","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210086872","https://openalex.org/I4210096427","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"A. Bahr","raw_affiliation_strings":["Laboratoire de Biologie et Genomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France","IGBMC - Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (Parc D'Innovation 1 Rue Laurent Fries - BP 10142 67404 Illkirch Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Biologie et Genomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I1294671590","https://openalex.org/I4210086872"]},{"raw_affiliation_string":"IGBMC - Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (Parc D'Innovation 1 Rue Laurent Fries - BP 10142 67404 Illkirch Cedex - France)","institution_ids":["https://openalex.org/I4210086872"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077028466"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210086872"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":1.862,"has_fulltext":false,"cited_by_count":193,"citation_normalized_percentile":{"value":0.85463116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"29","issue":"1","first_page":"323","last_page":"326"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6788336634635925},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6547285318374634},{"id":"https://openalex.org/keywords/file-transfer-protocol","display_name":"File Transfer Protocol","score":0.6393827199935913},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6186402440071106},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5254886746406555},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.497927188873291},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4033198952674866},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35778772830963135},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3056263029575348},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18545258045196533},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0777791440486908},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.07063296437263489}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6788336634635925},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6547285318374634},{"id":"https://openalex.org/C169485995","wikidata":"https://www.wikidata.org/wiki/Q42283","display_name":"File Transfer Protocol","level":3,"score":0.6393827199935913},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6186402440071106},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5254886746406555},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.497927188873291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4033198952674866},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35778772830963135},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3056263029575348},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18545258045196533},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0777791440486908},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.07063296437263489},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/29.1.323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/29.1.323","pdf_url":"https://academic.oup.com/nar/article-pdf/29/1/323/9905805/290323.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:11125126","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11125126","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:HAL:hal-04094322v1","is_oa":false,"landing_page_url":"https://hal.science/hal-04094322","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 2001, 29 (1), pp.323-326. &#x27E8;10.1093/nar/29.1.323&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:280158","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC29792","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:29792","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/29792","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/29.1.323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/29.1.323","pdf_url":"https://academic.oup.com/nar/article-pdf/29/1/323/9905805/290323.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1969051510","https://openalex.org/W1987393189","https://openalex.org/W2039105249","https://openalex.org/W2092670169","https://openalex.org/W2094104050","https://openalex.org/W2097747021","https://openalex.org/W2115840790","https://openalex.org/W2117919289","https://openalex.org/W2126405180","https://openalex.org/W2131227307","https://openalex.org/W2140292630","https://openalex.org/W2141411672","https://openalex.org/W2141513355","https://openalex.org/W2141885858","https://openalex.org/W2154352662","https://openalex.org/W2155755608","https://openalex.org/W2158714788","https://openalex.org/W2163860567","https://openalex.org/W4252166161"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2153373894","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W2495707678","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307"],"abstract_inverted_index":{"BAliBASE":[0,110],"is":[1],"specifically":[2],"designed":[3],"to":[4,10,98],"serve":[5],"as":[6],"an":[7],"evaluation":[8],"resource":[9],"address":[11],"all":[12,37],"the":[13,44,47,60,80,100,115],"problems":[14,61],"encountered":[15],"when":[16],"aligning":[17],"complete":[18],"sequences.":[19,49,109],"The":[20,34,50],"database":[21],"contains":[22],"high":[23,63],"quality,":[24],"manually":[25],"constructed":[26],"multiple":[27],"sequence":[28],"alignments":[29,35,57,89],"together":[30],"with":[31,43,59],"detailed":[32],"annotations.":[33],"are":[36],"based":[38],"on":[39],"three-dimensional":[40],"structural":[41,91],"superpositions,":[42],"exception":[45],"of":[46,55,62,79,88,102,106],"transmembrane":[48],"first":[51],"release":[52],"provided":[53],"sets":[54,87],"reference":[56,86],"dealing":[58],"variability,":[64],"unequal":[65],"repartition":[66],"and":[67,71,95,104],"large":[68],"N/C-terminal":[69],"extensions":[70],"internal":[72],"insertions.":[73],"Here":[74],"we":[75],"describe":[76],"version":[77],"2.0":[78],"database,":[81],"which":[82],"incorporates":[83],"three":[84],"new":[85],"containing":[90],"repeats,":[92],"trans-membrane":[93],"sequences":[94],"circular":[96],"permutations":[97],"evaluate":[99],"accuracy":[101],"detection/prediction":[103],"alignment":[105],"these":[107],"complex":[108],"can":[111,121],"be":[112,122],"viewed":[113],"at":[114],"web":[116],"site":[117],"http://www-igbmc.u-strasbg.":[118],"fr/BioInfo/BAliBASE2/index.html":[119],"or":[120],"downloaded":[123],"from":[124],"ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2":[125],"/.":[126]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
