{"id":"https://openalex.org/W1974983026","doi":"https://doi.org/10.1093/bioinformatics/btm635","title":"Colorstock, SScolor, Rat\u00f3n: RNA alignment visualization tools","display_name":"Colorstock, SScolor, Rat\u00f3n: RNA alignment visualization tools","publication_year":2008,"publication_date":"2008-01-24","ids":{"openalex":"https://openalex.org/W1974983026","doi":"https://doi.org/10.1093/bioinformatics/btm635","mag":"1974983026","pmid":"https://pubmed.ncbi.nlm.nih.gov/18218657"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm635","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm635","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/579/49045695/bioinformatics_24_4_579.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/24/4/579/49045695/bioinformatics_24_4_579.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001496158","display_name":"Yuri R. Benda\u00f1a","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuri R. Benda\u00f1a","raw_affiliation_strings":["Department of Bioengineering, UC Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, UC Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ian H. Holmes","raw_affiliation_strings":["Department of Bioengineering, UC Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, UC Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054625887"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.6638,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67393756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"24","issue":"4","first_page":"579","last_page":"580"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5830000042915344,"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":0.5830000042915344,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.09669999778270721,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.08209999650716782,"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/computer-science","display_name":"Computer science","score":0.7389237880706787},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.6753948330879211},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.654363214969635},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.581974446773529},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5458536148071289},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.44215893745422363},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.42098474502563477},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.41224151849746704},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3355611264705658},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32833361625671387},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18407782912254333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1756979525089264},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1379709541797638},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07770320773124695}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7389237880706787},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6753948330879211},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.654363214969635},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.581974446773529},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5458536148071289},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.44215893745422363},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.42098474502563477},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.41224151849746704},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3355611264705658},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32833361625671387},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18407782912254333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1756979525089264},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1379709541797638},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07770320773124695},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btm635","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm635","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/579/49045695/bioinformatics_24_4_579.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:18218657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18218657","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"},{"id":"pmh:oai:europepmc.org:6068203","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7109877","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"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.320.4125","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.320.4125","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://biowiki.org/~yam/Papers/BendanaHolmes2008-Colorstock.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.562.8162","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.562.8162","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2008/01/24/bioinformatics.btm635.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm635","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm635","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/579/49045695/bioinformatics_24_4_579.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":[{"id":"https://openalex.org/G4670916211","display_name":null,"funder_award_id":"R01-GM076705","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7218059032","display_name":null,"funder_award_id":"1R01GM076705-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1974983026.pdf","grobid_xml":"https://content.openalex.org/works/W1974983026.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1856600885","https://openalex.org/W2020021066","https://openalex.org/W2108770512","https://openalex.org/W2134408611","https://openalex.org/W2140302584","https://openalex.org/W2158381555","https://openalex.org/W2158654777","https://openalex.org/W2158826174","https://openalex.org/W2159738351"],"related_works":["https://openalex.org/W2480056510","https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W2613359208","https://openalex.org/W2291334382","https://openalex.org/W4249676448"],"abstract_inverted_index":{"UNLABELLED:":[0],"Interactive":[1],"examination":[2],"of":[3,24,94],"RNA":[4,16,26,62],"multiple":[5],"alignments":[6,63],"for":[7],"covariant":[8],"mutations":[9,72],"is":[10,79],"a":[11,30,38,92],"useful":[12],"step":[13],"in":[14,73],"non-coding":[15],"sequence":[17],"analysis.":[18],"We":[19],"present":[20],"three":[21],"parallel":[22],"implementations":[23],"an":[25,48],"visualization":[27],"metaphor:":[28],"Colorstock,":[29],"command-line":[31],"script":[32,40],"using":[33],"ANSI":[34],"terminal":[35],"color;":[36],"SScolor,":[37],"Perl":[39],"that":[41],"generates":[42],"static":[43],"HTML":[44],"pages;":[45],"and":[46,67,91],"Rat\u00f3n,":[47],"AJAX":[49],"web":[50],"application":[51],"generating":[52],"dynamic":[53],"HTML.":[54],"Each":[55],"tool":[56],"can":[57,88,96],"be":[58,89,97],"used":[59],"to":[60,68],"color":[61],"by":[64],"secondary":[65],"structure":[66],"visually":[69],"highlight":[70],"compensatory":[71],"stems.":[74],"AVAILABILITY:":[75],"All":[76],"source":[77,86],"code":[78,87],"freely":[80],"available":[81],"under":[82],"the":[83],"GPL.":[84],"The":[85],"downloaded":[90],"prototype":[93],"Rat\u00f3n":[95],"accessed":[98],"at":[99],"http://biowiki.org/RnaAlignmentViewers.":[100]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
