{"id":"https://openalex.org/W2100905897","doi":"https://doi.org/10.1093/bioinformatics/bts667","title":"DOOSS: a tool for visual analysis of data overlaid on secondary structures","display_name":"DOOSS: a tool for visual analysis of data overlaid on secondary structures","publication_year":2012,"publication_date":"2012-11-21","ids":{"openalex":"https://openalex.org/W2100905897","doi":"https://doi.org/10.1093/bioinformatics/bts667","mag":"2100905897","pmid":"https://pubmed.ncbi.nlm.nih.gov/23172861"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/271/48890629/bioinformatics_29_2_271.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/29/2/271/48890629/bioinformatics_29_2_271.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013116981","display_name":"Michael Golden","orcid":"https://orcid.org/0000-0002-3653-8019"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Michael Golden","raw_affiliation_strings":["Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa","institution_ids":["https://openalex.org/I157614274"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064593386","display_name":"Darren P. Martin","orcid":"https://orcid.org/0000-0002-8785-0870"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"education","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Darren Martin","raw_affiliation_strings":["Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa","institution_ids":["https://openalex.org/I157614274"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013116981"],"corresponding_institution_ids":["https://openalex.org/I157614274"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.246,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.55433212,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"29","issue":"2","first_page":"271","last_page":"272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.1680999994277954,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.1680999994277954,"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":0.14079999923706055,"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":0.11720000207424164,"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/java","display_name":"Java","score":0.6766732931137085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6688563823699951},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5813153982162476},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.49622613191604614},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4447647035121918},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.43987351655960083},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4332910180091858},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39587679505348206},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32650691270828247},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.25603917241096497},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2444533407688141},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21751472353935242},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1034749448299408}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6766732931137085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6688563823699951},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5813153982162476},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.49622613191604614},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4447647035121918},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.43987351655960083},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4332910180091858},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39587679505348206},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32650691270828247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25603917241096497},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2444533407688141},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21751472353935242},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1034749448299408},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"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":"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/271/48890629/bioinformatics_29_2_271.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:23172861","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23172861","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/271/48890629/bioinformatics_29_2_271.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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100905897.pdf","grobid_xml":"https://content.openalex.org/works/W2100905897.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2009736453","https://openalex.org/W2032136448","https://openalex.org/W2132926880","https://openalex.org/W2143407915","https://openalex.org/W2147427891","https://openalex.org/W2400250419"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2085384747","https://openalex.org/W2077542787","https://openalex.org/W2749690376","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W4281673905","https://openalex.org/W2106071040"],"abstract_inverted_index":{"MOTIVATION:":[0],"DOOSS":[1,48],"(Data":[2],"Overlaid":[3],"On":[4],"Secondary":[5],"Structures)":[6],"is":[7,30,49,54],"a":[8],"tool":[9,29],"for":[10],"visualizing":[11],"annotated":[12],"secondary":[13,40],"structures":[14,41],"of":[15,27,39],"large":[16],"single-stranded":[17],"nucleotide":[18],"sequences":[19],"(such":[20],"as":[21],"full-length":[22],"virus":[23],"genomes).":[24],"The":[25],"purpose":[26],"this":[28],"to":[31],"assist":[32],"investigators":[33],"in":[34,51],"evaluating":[35],"the":[36],"biological":[37],"relevance":[38],"within":[42],"particular":[43],"sequences.":[44],"AVAILABILITY":[45],"AND":[46],"IMPLEMENTATION:":[47],"written":[50],"Java":[52],"and":[53],"available":[55,65],"from:":[56],"http://dooss.computingforbiology.org":[57],"CONTACT:":[58],"michaelgolden0@gmail.com":[59],"SUPPLEMENTARY":[60],"INFORMATION:":[61],"Supplementary":[62],"data":[63],"are":[64],"at":[66],"Bioinformatics":[67],"online.":[68]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
