{"id":"https://openalex.org/W2107455994","doi":"https://doi.org/10.1016/s1672-0229(10)60015-0","title":"BiDiBlast: Comparative Genomics Pipeline for the PC","display_name":"BiDiBlast: Comparative Genomics Pipeline for the PC","publication_year":2010,"publication_date":"2010-06-01","ids":{"openalex":"https://openalex.org/W2107455994","doi":"https://doi.org/10.1016/s1672-0229(10)60015-0","mag":"2107455994","pmid":"https://pubmed.ncbi.nlm.nih.gov/20691399"},"language":"en","primary_location":{"id":"doi:10.1016/s1672-0229(10)60015-0","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(10)60015-0","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022910600150/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.sciencedirect.com/science/article/pii/S1672022910600150/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055639768","display_name":"Jo\u00e3o M. G. C. F. Almeida","orcid":"https://orcid.org/0000-0003-2965-6268"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Jo\u00e3o M.G.C.F. de Almeida","raw_affiliation_strings":["Centro de Recursos Microbiol\u00f3gicos (CREM), Departamento de Ci\u00eancias da Vida, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa , Caparica, Quinta da Torre, 2829-516 , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Recursos Microbiol\u00f3gicos (CREM), Departamento de Ci\u00eancias da Vida, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa , Caparica, Quinta da Torre, 2829-516 , Portugal","institution_ids":["https://openalex.org/I83558840"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055639768"],"corresponding_institution_ids":["https://openalex.org/I83558840"],"apc_list":{"value":3650,"currency":"USD","value_usd":3650},"apc_paid":{"value":3650,"currency":"USD","value_usd":3650},"fwci":0.1245,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.51622624,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"8","issue":"2","first_page":"135","last_page":"138"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9959999918937683,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9894999861717224,"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/perl","display_name":"Perl","score":0.9578466415405273},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.792174220085144},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7479220628738403},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.6869831085205078},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.6217551231384277},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.590404748916626},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5756518244743347},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5366954207420349},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5039111971855164},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.48821237683296204},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.47331130504608154},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4599532186985016},{"id":"https://openalex.org/keywords/code-refactoring","display_name":"Code refactoring","score":0.44562095403671265},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.4349735975265503},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3387332558631897}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.9578466415405273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.792174220085144},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7479220628738403},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.6869831085205078},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.6217551231384277},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.590404748916626},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5756518244743347},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5366954207420349},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5039111971855164},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.48821237683296204},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.47331130504608154},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4599532186985016},{"id":"https://openalex.org/C152752567","wikidata":"https://www.wikidata.org/wiki/Q116877","display_name":"Code refactoring","level":3,"score":0.44562095403671265},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.4349735975265503},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3387332558631897},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008838","descriptor_name":"Microcomputers","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1016/s1672-0229(10)60015-0","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(10)60015-0","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022910600150/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20691399","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20691399","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4016597","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054440","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/s1672-0229(10)60015-0","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(10)60015-0","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022910600150/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2107455994.pdf","grobid_xml":"https://content.openalex.org/works/W2107455994.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1990453950","https://openalex.org/W1996423252","https://openalex.org/W2003144438","https://openalex.org/W2055043387","https://openalex.org/W2059123697","https://openalex.org/W2100827887","https://openalex.org/W2101783948","https://openalex.org/W2108215151","https://openalex.org/W2110335151","https://openalex.org/W2115011276","https://openalex.org/W2150261709","https://openalex.org/W4213149192","https://openalex.org/W6675949863"],"related_works":["https://openalex.org/W2475789275","https://openalex.org/W2356222173","https://openalex.org/W2745097874","https://openalex.org/W2508823388","https://openalex.org/W2391811762","https://openalex.org/W2225951319","https://openalex.org/W645133142","https://openalex.org/W2992663142","https://openalex.org/W634263678","https://openalex.org/W2038005706"],"abstract_inverted_index":{"Bi-directional":[0],"BLAST":[1,84],"is":[2,22,143],"a":[3,17,64,120,136],"simple":[4,94],"approach":[5],"to":[6,25,40,78,101,119,147],"detect,":[7],"annotate,":[8],"and":[9,47,89,93,107,145],"analyze":[10],"candidate":[11],"orthologous":[12],"or":[13,151],"paralogous":[14],"sequences":[15,77],"in":[16,69],"single":[18],"go.":[19],"This":[20,71],"procedure":[21],"usually":[23,32],"confined":[24],"the":[26,49,52,57,82,154],"realm":[27],"of":[28,51,76,81,122],"customized":[29],"Perl":[30,53],"scripts,":[31],"tuned":[33],"for":[34,127],"UNIX-like":[35],"environments.":[36],"Porting":[37],"those":[38],"scripts":[39],"other":[41],"operating":[42],"systems":[43],"involves":[44],"refactoring":[45],"them,":[46],"also":[48],"installation":[50],"programming":[54],"environment":[55],"with":[56,139],"required":[58],"libraries.":[59],"To":[60],"overcome":[61],"these":[62],"limitations,":[63],"data":[65],"pipeline":[66],"was":[67],"implemented":[68],"Java.":[70],"application":[72],"submits":[73],"two":[74],"batches":[75],"local":[79],"versions":[80],"NCBI":[83],"tool,":[85],"manages":[86],"result":[87],"lists,":[88],"refines":[90],"both":[91],"bi-directional":[92],"hits.":[95],"GO":[96],"Slim":[97],"terms":[98],"are":[99,105,111,117],"attached":[100],"hits,":[102],"several":[103],"statistics":[104],"derived,":[106],"molecular":[108],"evolution":[109],"rates":[110],"estimated":[112],"through":[113],"PAML.":[114],"The":[115,130],"results":[116],"written":[118],"set":[121],"delimited":[123],"text":[124],"tables":[125],"intended":[126],"further":[128],"analysis.":[129],"provided":[131],"graphic":[132],"user":[133],"interface":[134],"allows":[135],"friendly":[137],"interaction":[138],"this":[140],"application,":[141],"which":[142],"documented":[144],"available":[146],"download":[148],"at":[149],"http://moodle.fct.unl.pt/course/view.php?id=2079":[150],"https://sourceforge.net/projects/bidiblast/":[152],"under":[153],"GNU":[155],"GPL":[156],"license.":[157]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
