{"id":"https://openalex.org/W2171164011","doi":"https://doi.org/10.1093/bioinformatics/btg406","title":"JDotter: a Java interface to multiple dotplots generated by dotter","display_name":"JDotter: a Java interface to multiple dotplots generated by dotter","publication_year":2004,"publication_date":"2004-01-20","ids":{"openalex":"https://openalex.org/W2171164011","doi":"https://doi.org/10.1093/bioinformatics/btg406","mag":"2171164011","pmid":"https://pubmed.ncbi.nlm.nih.gov/14734323"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg406","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/279/48905137/bioinformatics_20_2_279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/article-pdf/20/2/279/48905137/bioinformatics_20_2_279.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010643968","display_name":"Ryan Brodie","orcid":null},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Ryan Brodie","raw_affiliation_strings":["Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053962751","display_name":"Rachel L. Roper","orcid":"https://orcid.org/0000-0001-6971-7745"},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Rachel L. Roper","raw_affiliation_strings":["Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada","institution_ids":["https://openalex.org/I212119943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033180528","display_name":"Chris Upton","orcid":"https://orcid.org/0000-0002-9019-8967"},"institutions":[{"id":"https://openalex.org/I212119943","display_name":"University of Victoria","ror":"https://ror.org/04s5mat29","country_code":"CA","type":"education","lineage":["https://openalex.org/I212119943"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chris Upton","raw_affiliation_strings":["Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada","institution_ids":["https://openalex.org/I212119943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010643968"],"corresponding_institution_ids":["https://openalex.org/I212119943"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3409,"has_fulltext":true,"cited_by_count":129,"citation_normalized_percentile":{"value":0.89231161,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"20","issue":"2","first_page":"279","last_page":"281"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.1257999986410141,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.1257999986410141,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.11630000174045563,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.10249999910593033,"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/java","display_name":"Java","score":0.7759166955947876},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.7351611852645874},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6360939741134644},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48355790972709656},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4484706223011017},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3427833318710327},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2705785036087036}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7759166955947876},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.7351611852645874},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6360939741134644},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48355790972709656},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4484706223011017},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3427833318710327},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2705785036087036},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg406","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/279/48905137/bioinformatics_20_2_279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:14734323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14734323","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg406","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/279/48905137/bioinformatics_20_2_279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4300000071525574}],"awards":[{"id":"https://openalex.org/G1248344000","display_name":null,"funder_award_id":"U01AI48653-02","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171164011.pdf","grobid_xml":"https://content.openalex.org/works/W2171164011.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2035625064","https://openalex.org/W2106880273","https://openalex.org/W2138334294","https://openalex.org/W2157307853"],"related_works":["https://openalex.org/W2749690376","https://openalex.org/W2786317006","https://openalex.org/W4367724653","https://openalex.org/W2788563018","https://openalex.org/W2997587123","https://openalex.org/W4281673905","https://openalex.org/W3206385231","https://openalex.org/W2381929017","https://openalex.org/W2369108811","https://openalex.org/W2736583656"],"abstract_inverted_index":{"UNLABELLED:":[0],"Java-Dotter":[1],"(JDotter)":[2],"is":[3,95,116,147],"a":[4,15,31,50,59,89],"platform-independent":[5],"Java":[6,98],"interactive":[7],"interface":[8],"for":[9,19,43,106,118,149],"the":[10,40,102,121,128,137],"Linux":[11],"version":[12],"of":[13,22,52,85,109],"Dotter,":[14],"widely":[16],"used":[17,96],"program":[18,42],"generating":[20],"dotplots":[21,108],"large":[23,83],"DNA":[24],"or":[25,62],"protein":[26],"sequences.":[27],"JDotter":[28,55,71,94,138],"runs":[29],"as":[30,45,47],"client-server":[32],"application":[33],"and":[34,87,132,144],"can":[35],"send":[36],"new":[37],"sequences":[38],"to":[39,65,75],"Dotter":[41],"alignment":[44],"well":[46],"rapidly":[48],"access":[49,74],"repository":[51],"preprocessed":[53],"dotplots.":[54],"also":[56],"interfaces":[57],"with":[58,82],"sequence":[60],"database":[61],"file":[63],"system":[64],"display":[66],"supplementary":[67],"feature":[68],"data.":[69],"Thus,":[70],"greatly":[72],"simplifies":[73],"dotplot":[76],"data":[77],"in":[78],"laboratories":[79],"that":[80],"deal":[81],"numbers":[84],"genomes":[86],"have":[88],"multi-platform":[90],"organization.":[91],"AVAILABILITY:":[92],"Currently,":[93],"via":[97],"Web":[99],"Start":[100],"by":[101],"Poxvirus":[103],"Bioinformatics":[104],"Resource":[105],"examining":[107],"complete":[110],"poxvirus":[111],"genomes;":[112],"http://athena.bioc.uvic.ca/pbr/jdotter/.":[113,141],"The":[114,142],"software":[115,143],"available":[117,135],"download":[119],"from":[120],"same":[122],"location.":[123],"SUPPLEMENTARY":[124],"INFORMATION:":[125],"Installation":[126],"instructions,":[127],"User's":[129],"Manual,":[130],"screenshots":[131],"examples":[133],"are":[134],"at":[136],"home":[139],"page":[140],"source":[145],"code":[146],"free":[148],"non-commercial":[150],"applications.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
