{"id":"https://openalex.org/W2903801233","doi":"https://doi.org/10.1093/bioinformatics/bty1013","title":"MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment","display_name":"MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment","publication_year":2018,"publication_date":"2018-12-06","ids":{"openalex":"https://openalex.org/W2903801233","doi":"https://doi.org/10.1093/bioinformatics/bty1013","mag":"2903801233","pmid":"https://pubmed.ncbi.nlm.nih.gov/30535283"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty1013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2671/29012405/bty1013.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/35/15/2671/29012405/bty1013.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057303658","display_name":"Josephine Burgin","orcid":"https://orcid.org/0000-0002-9818-1094"},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Josephine Burgin","raw_affiliation_strings":["The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK","institution_ids":["https://openalex.org/I82284825"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032525558","display_name":"Corentin Molitor","orcid":"https://orcid.org/0000-0003-2569-6764"},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Corentin Molitor","raw_affiliation_strings":["The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK","institution_ids":["https://openalex.org/I82284825"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060147540","display_name":"Fady Mohareb","orcid":"https://orcid.org/0000-0002-7880-2519"},"institutions":[{"id":"https://openalex.org/I82284825","display_name":"Cranfield University","ror":"https://ror.org/05cncd958","country_code":"GB","type":"education","lineage":["https://openalex.org/I82284825"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Fady Mohareb","raw_affiliation_strings":["The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Bioinformatics Group, Cranfield Soil and Agrifood Institute, School of Water, Energy and Environment, Cranfield University, Bedford MK43 0AL, UK","institution_ids":["https://openalex.org/I82284825"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5060147540"],"corresponding_institution_ids":["https://openalex.org/I82284825"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4952,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.62906437,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"35","issue":"15","first_page":"2671","last_page":"2673"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6474000215530396,"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":0.6474000215530396,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.05420000106096268,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.03550000116229057,"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":0.792732834815979},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.757646918296814},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7475506067276001},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5033759474754333},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.35360366106033325},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3128282427787781},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3006756007671356}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.792732834815979},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.757646918296814},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7475506067276001},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5033759474754333},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.35360366106033325},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3128282427787781},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3006756007671356}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","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":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty1013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2671/29012405/bty1013.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:30535283","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30535283","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},{"id":"pmh:oai:dspace.lib.cranfield.ac.uk:1826/13711","is_oa":true,"landing_page_url":"http://dspace.lib.cranfield.ac.uk/handle/1826/13711","pdf_url":null,"source":{"id":"https://openalex.org/S4306401778","display_name":"CERES (Cranfield University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I82284825","host_organization_name":"Cranfield University","host_organization_lineage":["https://openalex.org/I82284825"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty1013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1013","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2671/29012405/bty1013.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/G3387449359","display_name":"Genomics-assisted selection of Solanum chilense introgression lines for enhancing drought resistance in tomatoes","funder_award_id":"BB/L011611/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7347109709","display_name":null,"funder_award_id":"BB/L011611/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1791377616","https://openalex.org/W2167155938","https://openalex.org/W2527708324","https://openalex.org/W2590583044","https://openalex.org/W2594267054","https://openalex.org/W2611920982","https://openalex.org/W2613329041","https://openalex.org/W2779945812","https://openalex.org/W2791398042","https://openalex.org/W3103208583"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2749690376","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W4281673905","https://openalex.org/W2736583656"],"abstract_inverted_index":{"SUMMARY:":[0],"Bionano":[1,75],"optical":[2,76,100],"mapping":[3,77,101],"is":[4,58,115],"a":[5,23,31,44,59,93,141],"technology":[6],"that":[7,63],"can":[8,80,127],"assist":[9],"in":[10,22,84,117],"the":[11,28,65,72,98],"final":[12],"stages":[13],"of":[14,74,87,109],"genome":[15],"assembly":[16,25,29],"by":[17,26],"lengthening":[18],"and":[19,69,79,120,132],"ordering":[20],"scaffolds":[21],"draft":[24],"aligning":[27],"to":[30,41,67,97],"genomic":[32],"map.":[33],"However,":[34],"currently,":[35],"tools":[36],"for":[37,52,83,106],"visualization":[38],"are":[39,49,150],"limited":[40],"use":[42],"on":[43,134],"Windows":[45],"operating":[46],"system":[47],"or":[48],"developed":[50],"initially":[51],"visualizing":[53],"large-scale":[54],"structural":[55],"variation.":[56],"MapOptics":[57,114,126],"lightweight":[60],"cross-platform":[61],"tool":[62],"enables":[64],"user":[66],"visualize":[68],"interact":[70],"with":[71,140],"alignment":[73],"data":[78,149],"be":[81,128],"used":[82],"depth":[85],"exploration":[86],"hybrid":[88],"scaffolding":[89],"alignments.":[90],"It":[91],"provides":[92],"fast,":[94],"simple":[95],"alternative":[96],"large":[99],"analysis":[102],"programs":[103],"currently":[104],"available":[105,151],"this":[107],"area":[108],"research.":[110],"AVAILABILITY":[111],"AND":[112],"IMPLEMENTATION:":[113],"implemented":[116],"Java":[118,142],"1.8":[119],"released":[121],"under":[122],"an":[123],"MIT":[124],"licence.":[125],"downloaded":[129],"from":[130],"https://github.com/FadyMohareb/mapoptics":[131],"run":[133],"any":[135],"standard":[136],"desktop":[137],"computer":[138],"equipped":[139],"Virtual":[143],"Machine":[144],"(JVM).":[145],"SUPPLEMENTARY":[146],"INFORMATION:":[147],"Supplementary":[148],"at":[152],"Bioinformatics":[153],"online.":[154]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}
