{"id":"https://openalex.org/W4412454232","doi":"https://doi.org/10.1093/bioinformatics/btaf225","title":"Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs","display_name":"Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454232","doi":"https://doi.org/10.1093/bioinformatics/btaf225","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662827"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf225","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf225","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101764985","display_name":"Nicola Rizzo","orcid":"https://orcid.org/0000-0002-2035-6309"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Nicola Rizzo","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki,"],"raw_orcid":"https://orcid.org/0000-0002-2035-6309","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki,","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064412838","display_name":"Manuel C\u00e1ceres","orcid":"https://orcid.org/0000-0003-0235-6951"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Manuel C\u00e1ceres","raw_affiliation_strings":["Department of Computer Science, Aalto University , 00076 Espoo,"],"raw_orcid":"https://orcid.org/0000-0003-0235-6951","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , 00076 Espoo,","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veli M\u00e4kinen","raw_affiliation_strings":["Department of Computer Science, University of Helsinki , 00014 Helsinki,"],"raw_orcid":"https://orcid.org/0000-0003-4454-1493","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , 00014 Helsinki,","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101764985"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14690169,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i265","last_page":"i274"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2766000032424927,"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":0.2766000032424927,"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":0.16050000488758087,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.10830000042915344,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.688787579536438},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.6392881870269775},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5887200832366943},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.564230740070343},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4679008722305298},{"id":"https://openalex.org/keywords/uniqueness","display_name":"Uniqueness","score":0.4457533657550812},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4192708134651184},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4131369888782501},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3424602746963501},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21262657642364502},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19033893942832947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18374103307724},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1472301483154297},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.09362539649009705}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.688787579536438},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.6392881870269775},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5887200832366943},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.564230740070343},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4679008722305298},{"id":"https://openalex.org/C2777021972","wikidata":"https://www.wikidata.org/wiki/Q22976830","display_name":"Uniqueness","level":2,"score":0.4457533657550812},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4192708134651184},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4131369888782501},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3424602746963501},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21262657642364502},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19033893942832947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18374103307724},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1472301483154297},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09362539649009705},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016615","descriptor_name":"Telomere","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf225","pdf_url":null,"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:40662827","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662827","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:pubmedcentral.nih.gov:12261467","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261467","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf225","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf225","pdf_url":null,"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":[{"id":"https://openalex.org/F1744609432","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W2072021854","https://openalex.org/W2074229180","https://openalex.org/W2103441770","https://openalex.org/W2158322625","https://openalex.org/W2522993044","https://openalex.org/W2617749016","https://openalex.org/W2789843538","https://openalex.org/W2810672408","https://openalex.org/W2888300707","https://openalex.org/W2889833303","https://openalex.org/W2929062889","https://openalex.org/W2952366981","https://openalex.org/W2964849163","https://openalex.org/W2971433408","https://openalex.org/W2989658460","https://openalex.org/W2999295646","https://openalex.org/W3010580865","https://openalex.org/W3017152484","https://openalex.org/W3086678357","https://openalex.org/W3088400220","https://openalex.org/W3092652421","https://openalex.org/W3099761377","https://openalex.org/W3120923229","https://openalex.org/W3131672637","https://openalex.org/W3181407718","https://openalex.org/W4200597270","https://openalex.org/W4205262153","https://openalex.org/W4206067192","https://openalex.org/W4220680041","https://openalex.org/W4220999759","https://openalex.org/W4247794781","https://openalex.org/W4285723210","https://openalex.org/W4308735750","https://openalex.org/W4321497857","https://openalex.org/W4327590906","https://openalex.org/W4362499343","https://openalex.org/W4376118380","https://openalex.org/W4385269543","https://openalex.org/W4386113054","https://openalex.org/W4387818211","https://openalex.org/W4388034820","https://openalex.org/W4389194970","https://openalex.org/W4393810622","https://openalex.org/W4396966282","https://openalex.org/W4403609447","https://openalex.org/W6966982515"],"related_works":["https://openalex.org/W571281153","https://openalex.org/W2949403936","https://openalex.org/W4301247218","https://openalex.org/W3023806604","https://openalex.org/W2952139525","https://openalex.org/W2129818458","https://openalex.org/W4289551052","https://openalex.org/W2340777379","https://openalex.org/W4390756076","https://openalex.org/W4243074410"],"abstract_inverted_index":{"SUMMARY:":[0],"Sequence-to-graph":[1],"alignment":[2,32,76],"is":[3],"a":[4,29,66],"central":[5],"challenge":[6],"of":[7,15,65],"computational":[8],"pangenomics.":[9],"To":[10],"overcome":[11],"the":[12,16,63,79],"theoretical":[13],"hardness":[14],"problem,":[17],"state-of-the-art":[18],"tools":[19],"use":[20],"seed-and-extend":[21],"or":[22],"seed-chain-extend":[23,31],"heuristics":[24],"to":[25,52,81],"alignment.":[26],"We":[27,49],"implement":[28],"complete":[30],"workflow":[33],"based":[34],"on":[35],"indexable":[36],"elastic":[37],"founder":[38],"graphs":[39],"(iEFGs)":[40],"that":[41],"support":[42],"linear-time":[43],"exact":[44],"searches":[45],"unlike":[46],"general":[47],"graphs.":[48],"show":[50],"how":[51],"construct":[53],"iEFGs,":[54],"find":[55],"high-quality":[56],"seeds,":[57],"chain,":[58],"and":[59,78],"extend":[60],"them":[61],"at":[62],"scale":[64],"telomere-to-telomere":[67],"assembled":[68],"human":[69],"chromosome.":[70],"AVAILABILITY":[71],"AND":[72],"IMPLEMENTATION:":[73],"Our":[74],"sequence-to-graph":[75],"tool":[77],"scripts":[80],"replicate":[82],"our":[83],"experiments":[84],"are":[85],"available":[86],"in":[87],"https://github.com/algbio/SRFAligner.":[88]},"counts_by_year":[],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
