{"id":"https://openalex.org/W2151405227","doi":"https://doi.org/10.1109/csb.2005.31","title":"Efficient algorithms and software for detection of full-length LTR retrotransposons","display_name":"Efficient algorithms and software for detection of full-length LTR retrotransposons","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W2151405227","doi":"https://doi.org/10.1109/csb.2005.31","mag":"2151405227","pmid":"https://pubmed.ncbi.nlm.nih.gov/16447962"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2005.31","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"proceedings-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014307317","display_name":"Anantharaman Kalyanaraman","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"funder","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Kalyanaraman","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074347913","display_name":"Srinivas Aluru","orcid":"https://orcid.org/0000-0003-4279-469X"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"funder","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Aluru","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.209,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":7,"citation_normalized_percentile":{"value":0.884236,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":79,"max":80},"biblio":{"volume":null,"issue":null,"first_page":"56","last_page":"64"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9996,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9996,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9982,"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":0.9951,"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/retrotransposon","display_name":"Retrotransposon","score":0.8927289}],"concepts":[{"id":"https://openalex.org/C7029365","wikidata":"https://www.wikidata.org/wiki/Q413988","display_name":"Retrotransposon","level":5,"score":0.8927289},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.690765},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5684128},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.55131024},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5192745},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5034849},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.43186706},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35016203},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34594202},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2662546},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20711339},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.17680067},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15567571},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13182789},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020079","descriptor_name":"Terminal Repeat Sequences","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020079","descriptor_name":"Terminal Repeat Sequences","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2005.31","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16447962","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":27,"referenced_works":["https://openalex.org/W117230746","https://openalex.org/W1489909987","https://openalex.org/W1490914592","https://openalex.org/W1495956867","https://openalex.org/W1554644662","https://openalex.org/W1928279239","https://openalex.org/W1953861638","https://openalex.org/W1990061958","https://openalex.org/W2005877477","https://openalex.org/W201532695","https://openalex.org/W2036676638","https://openalex.org/W2074231493","https://openalex.org/W2076092946","https://openalex.org/W2105052778","https://openalex.org/W2108336999","https://openalex.org/W2109289454","https://openalex.org/W2116628377","https://openalex.org/W2124281279","https://openalex.org/W2127384606","https://openalex.org/W2130564474","https://openalex.org/W2142204199","https://openalex.org/W2151899848","https://openalex.org/W2158874082","https://openalex.org/W2162216089","https://openalex.org/W2163960662","https://openalex.org/W4254745106","https://openalex.org/W938539187"],"related_works":["https://openalex.org/W4285312541","https://openalex.org/W4255017993","https://openalex.org/W4211158134","https://openalex.org/W2947397308","https://openalex.org/W2606486591","https://openalex.org/W2358072366","https://openalex.org/W2137282308","https://openalex.org/W2112373845","https://openalex.org/W2094923272","https://openalex.org/W1971924113"],"abstract_inverted_index":{"LTR":[0,27,45,76],"retrotransposons":[1,28],"constitute":[2],"one":[3],"of":[4,9,25,44,55,75,91,118,121,128],"the":[5,63,129,132],"most":[6],"abundant":[7],"classes":[8],"repetitive":[10],"elements":[11],"in":[12,29,36,67,78],"eukaryotic":[13],"genomes.":[14],"In":[15],"this":[16],"paper,":[17],"we":[18],"present":[19],"a":[20,37,58,87,101,115],"new":[21],"algorithm":[22,33,52,130],"for":[23],"detection":[24],"full-length":[26],"genomic":[30,38,65],"sequences.":[31],"The":[32],"identifies":[34],"regions":[35],"sequence":[39,66],"that":[40,54,61,81],"show":[41],"structural":[42,107],"characteristics":[43],"retrotransposons.":[46],"Three":[47],"key":[48],"components":[49],"distinguish":[50],"our":[51,123],"from":[53],"current":[56],"software-(i)":[57],"novel":[59],"method":[60],"preprocesses":[62],"entire":[64],"linear":[68],"time":[69,80],"and":[70,99,109,125,139],"produces":[71],"high":[72,96,116],"quality":[73,97,110,138],"pairs":[74,93],"candidates":[77],"running":[79],"is":[82],"constant":[83],"per":[84],"pair,":[85],"(ii)":[86],"thorough":[88],"alignment-based":[89],"evaluation":[90],"candidate":[92],"to":[94,144],"ensure":[95],"prediction,":[98],"(Hi)":[100],"robust":[102],"parameter":[103],"set":[104],"encompassing":[105],"both":[106,122,136],"constraints":[108],"controls":[111],"providing":[112],"users":[113],"with":[114],"degree":[117],"flexibility.":[119],"Validation":[120],"serial":[124],"parallel":[126],"implementations":[127],"against":[131],"yeast":[133],"genome":[134],"indicates":[135],"superior":[137],"performance":[140],"results":[141],"when":[142],"compared":[143],"existing":[145],"software.":[146]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2151405227","counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-02-23T07:27:59.849403","created_date":"2016-06-24"}