{"id":"https://openalex.org/W2058415829","doi":"https://doi.org/10.1093/bioinformatics/btl263","title":"Indel seeds for homology search","display_name":"Indel seeds for homology search","publication_year":2006,"publication_date":"2006-07-15","ids":{"openalex":"https://openalex.org/W2058415829","doi":"https://doi.org/10.1093/bioinformatics/btl263","mag":"2058415829","pmid":"https://pubmed.ncbi.nlm.nih.gov/16873491"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e341/617355/btl263.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/22/14/e341/617355/btl263.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111534014","display_name":"Denise Mak","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Denise Mak","raw_affiliation_strings":["Graduate Program in Bioinformatics, Boston University 1 \u00a0 1 \u00a0 \u00a0 Boston, MA 02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Program in Bioinformatics, Boston University 1 \u00a0 1 \u00a0 \u00a0 Boston, MA 02215","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017818645","display_name":"Yevgeniy Gelfand","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yevgeniy Gelfand","raw_affiliation_strings":["Lab for Biocomputing and Informatics, Boston University 2 \u00a0 2 \u00a0 \u00a0 Boston, MA 02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lab for Biocomputing and Informatics, Boston University 2 \u00a0 2 \u00a0 \u00a0 Boston, MA 02215","institution_ids":["https://openalex.org/I111088046","https://openalex.org/I4210151352"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065328235","display_name":"Gary Benson","orcid":"https://orcid.org/0000-0003-2374-5462"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary Benson","raw_affiliation_strings":["Department of Computer Science, Department of Biology, Boston University 3 \u00a0 3 \u00a0 \u00a0 Boston, MA 02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Department of Biology, Boston University 3 \u00a0 3 \u00a0 \u00a0 Boston, MA 02215","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5111534014"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4159,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.88312861,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"14","first_page":"e341","last_page":"e349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/indel","display_name":"Indel","score":0.9811139106750488},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.7728680372238159},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6076344847679138},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5990108251571655},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5441315174102783},{"id":"https://openalex.org/keywords/tandem-repeat","display_name":"Tandem repeat","score":0.5212593674659729},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49806880950927734},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49794888496398926},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.42949971556663513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35669130086898804},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18619218468666077},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12145569920539856}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.9811139106750488},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.7728680372238159},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6076344847679138},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5990108251571655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5441315174102783},{"id":"https://openalex.org/C27149982","wikidata":"https://www.wikidata.org/wiki/Q3456514","display_name":"Tandem repeat","level":4,"score":0.5212593674659729},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49806880950927734},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49794888496398926},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.42949971556663513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35669130086898804},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18619218468666077},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12145569920539856},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"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":"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012091","descriptor_name":"Repetitive Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btl263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e341/617355/btl263.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:16873491","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16873491","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:CiteSeerX.psu:10.1.1.114.8296","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.114.8296","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/cgi/reprint/22/14/e341.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.304.7113","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.304.7113","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/cgi/reprint/22/14/e341.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/14/e341/617355/btl263.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":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1989100825","https://openalex.org/W2015292449","https://openalex.org/W2024811036","https://openalex.org/W2055043387","https://openalex.org/W2101664494","https://openalex.org/W2106811687","https://openalex.org/W2109692166","https://openalex.org/W2112664161","https://openalex.org/W2112814753","https://openalex.org/W2114611642","https://openalex.org/W2128591967","https://openalex.org/W2129497695","https://openalex.org/W2131010376","https://openalex.org/W2133903964","https://openalex.org/W2136145671","https://openalex.org/W2139371638","https://openalex.org/W2158714788","https://openalex.org/W3021319303"],"related_works":["https://openalex.org/W1971376828","https://openalex.org/W2135846417","https://openalex.org/W2167094946","https://openalex.org/W4206406917","https://openalex.org/W2080028493","https://openalex.org/W2046457574","https://openalex.org/W3103976079","https://openalex.org/W4387460329","https://openalex.org/W1482222085","https://openalex.org/W2107335609"],"abstract_inverted_index":{"We":[0,166,195],"are":[1,136],"interested":[2],"in":[3,128,215],"detecting":[4,25],"homologous":[5,77,146],"genomic":[6,132],"DNA":[7],"sequences":[8,115],"with":[9],"the":[10,60,66,118,129,174,197,216],"goal":[11],"of":[12,68,76,117,131,145,176,200],"locating":[13],"approximate":[14],"inverted,":[15],"interspersed,":[16],"and":[17,35,87,94,103,152,180,188,204,222],"tandem":[18],"repeats.":[19],"Standard":[20],"search":[21,211],"techniques":[22],"start":[23],"by":[24],"small":[26],"matching":[27],"parts,":[28],"called":[29,159],"seeds,":[30,161],"between":[31],"a":[32,74,143,155,168,210],"query":[33],"sequence":[34,78,133,147],"database":[36],"sequences.":[37],"Contiguous":[38],"seed":[39,70,157,179],"models":[40],"have":[41,90],"existed":[42],"for":[43,112,126,172,212],"many":[44],"years.":[45],"Recently,":[46],"spaced":[47,86,189,223],"seeds":[48,57,89,184,190,203],"were":[49],"shown":[50],"to":[51],"be":[52,81],"more":[53],"sensitive":[54],"than":[55],"contiguous":[56,88,187],"without":[58],"increasing":[59],"random":[61],"hit":[62],"rate.":[63],"To":[64],"determine":[65],"superiority":[67],"one":[69],"model":[71,75,144],"over":[72],"another,":[73],"alignment":[79,148],"must":[80],"chosen.":[82],"Previous":[83],"studies":[84],"evaluating":[85],"assumed":[91],"that":[92,182],"matches":[93],"mismatches":[95],"occur":[96],"within":[97],"these":[98],"alignments,":[99],"but":[100,121],"not":[101],"insertions":[102],"deletions":[104],"(indels).":[105],"This":[106],"is":[107,122],"perhaps":[108],"appropriate":[109],"when":[110,124,191],"searching":[111],"protein":[113],"coding":[114],"(<5%":[116],"human":[119],"genome),":[120],"inappropriate":[123],"looking":[125],"repeats":[127,214],"majority":[130],"where":[134],"indels":[135,151],"common.":[137],"In":[138],"this":[139],"paper,":[140],"we":[141,153,206],"assume":[142],"which":[149,162],"includes":[150],"describe":[154],"new":[156],"model,":[158],"indel":[160,178,183,202,221],"explicitly":[163],"allows":[164],"indels.":[165,194],"present":[167,207],"waiting":[169],"time":[170],"formula":[171],"computing":[173],"sensitivity":[175],"an":[177],"show":[181],"significantly":[185],"outperform":[186],"homologies":[192],"include":[193],"discuss":[196],"practical":[198],"aspect":[199],"using":[201,219],"finally":[205],"results":[208],"from":[209],"inverted":[213],"dog":[217],"genome":[218],"both":[220],"seeds.":[224]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}