{"id":"https://openalex.org/W4414369533","doi":"https://doi.org/10.1093/bioinformatics/btaf504","title":"PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences","display_name":"PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences","publication_year":2025,"publication_date":"2025-09-15","ids":{"openalex":"https://openalex.org/W4414369533","doi":"https://doi.org/10.1093/bioinformatics/btaf504","pmid":"https://pubmed.ncbi.nlm.nih.gov/40971860"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf504","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf504/64274703/btaf504.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf504/64274703/btaf504.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116867654","display_name":"Mariia Pospelova","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariia Pospelova","raw_affiliation_strings":["Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","Computer Science and Engineering Department, Pennsylvania State University, State College, PA 16802, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA 16802, United States","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005373810","display_name":"Yana Safonova","orcid":"https://orcid.org/0000-0002-9634-4216"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yana Safonova","raw_affiliation_strings":["Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","Huck Institutes of Life Science, Pennsylvania State University , State College, PA 16802,","Computer Science and Engineering Department, Pennsylvania State University, State College, PA 16802, United States"],"raw_orcid":"https://orcid.org/0000-0002-9634-4216","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering Department, Pennsylvania State University , State College, PA 16802,","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Huck Institutes of Life Science, Pennsylvania State University , State College, PA 16802,","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA 16802, United States","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5005373810"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4643,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.64348008,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.20669999718666077,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.20669999718666077,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12417","display_name":"Morphological variations and asymmetry","score":0.1177000030875206,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.11389999836683273,"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/python","display_name":"Python (programming language)","score":0.8429999947547913},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7789000272750854},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.529699981212616},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.3610999882221222},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.32519999146461487}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8429999947547913},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7789000272750854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7544000148773193},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.529699981212616},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42739999294281006},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37869998812675476},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3610999882221222},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.32519999146461487},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3109000027179718},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3041999936103821},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.28839999437332153},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2777999937534332},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2563999891281128}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":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":"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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf504","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf504/64274703/btaf504.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40971860","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40971860","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:europepmc.org:11324033","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12516306","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf504","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf504/64274703/btaf504.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/W4414369533.pdf","grobid_xml":"https://content.openalex.org/works/W4414369533.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2096218748","https://openalex.org/W2165891191","https://openalex.org/W2789843538","https://openalex.org/W2892689606","https://openalex.org/W2994888090","https://openalex.org/W4220999759","https://openalex.org/W4280621809","https://openalex.org/W4399121795","https://openalex.org/W4401386115","https://openalex.org/W4409283540"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Revealing":[1],"structural":[2,22,71],"variations":[3,23,72],"within":[4],"and":[5,15,29,68,85,95,121],"across":[6,73],"populations":[7],"is":[8,116,122],"crucial":[9],"for":[10,19,44,102],"understanding":[11],"their":[12,33],"diversification":[13],"mechanisms":[14],"roles.":[16],"Existing":[17],"tools":[18],"visualization":[20,46,83],"of":[21,47,50,65,70,82,99],"often":[24],"require":[25],"labor-intensive":[26],"figure":[27],"preparation":[28],"are":[30],"limited":[31],"in":[32],"ability":[34],"to":[35,108],"integrate":[36],"annotations.":[37],"RESULTS:":[38],"We":[39],"developed":[40],"PatchWorkPlot,":[41],"a":[42,59],"tool":[43,79],"automated":[45],"pairwise":[48],"alignments":[49],"multiple":[51],"annotated":[52],"sequences":[53],"as":[54],"dot":[55],"plots":[56,101],"combined":[57],"into":[58],"single":[60],"matrix.":[61],"PatchWorkPlot":[62,90,115],"enables":[63],"exploration":[64],"positions,":[66],"breakpoints,":[67],"architectures":[69],"two":[74],"or":[75],"more":[76],"sequences.":[77],"The":[78],"supports":[80],"customization":[81],"parameters":[84],"produces":[86],"high-resolution,":[87],"publication-ready":[88],"figures.":[89],"significantly":[91],"reduces":[92],"manual":[93],"work":[94],"simplifies":[96],"the":[97],"generation":[98],"complex":[100],"various":[103],"cases,":[104],"from":[105],"individual":[106],"loci":[107],"large-scale":[109],"comparative":[110],"projects.":[111],"AVAILABILITY":[112],"AND":[113],"IMPLEMENTATION:":[114],"implemented":[117],"using":[118],"Python":[119],"3":[120],"publicly":[123],"available":[124],"at":[125],"GitHub:":[126],"github.com/yana-safonova/PatchWorkPlot.":[127]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}