{"id":"https://openalex.org/W2051348758","doi":"https://doi.org/10.1186/1471-2105-9-112","title":"ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences","display_name":"ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences","publication_year":2008,"publication_date":"2008-02-22","ids":{"openalex":"https://openalex.org/W2051348758","doi":"https://doi.org/10.1186/1471-2105-9-112","mag":"2051348758","pmid":"https://pubmed.ncbi.nlm.nih.gov/18294369"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-112","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-112","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-112","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-112","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017566247","display_name":"Hisakazu Iwama","orcid":null},"institutions":[{"id":"https://openalex.org/I201933988","display_name":"Kagawa University","ror":"https://ror.org/04j7mzp05","country_code":"JP","type":"education","lineage":["https://openalex.org/I201933988"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hisakazu Iwama","raw_affiliation_strings":["Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. iwama@med.kagawa-u.ac.jp","Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan. iwama@med.kagawa-u.ac.jp","institution_ids":["https://openalex.org/I201933988"]},{"raw_affiliation_string":"Life Science Research Center, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan","institution_ids":["https://openalex.org/I201933988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002697966","display_name":"Yukio Hori","orcid":null},"institutions":[{"id":"https://openalex.org/I201933988","display_name":"Kagawa University","ror":"https://ror.org/04j7mzp05","country_code":"JP","type":"education","lineage":["https://openalex.org/I201933988"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yukio Hori","raw_affiliation_strings":["Information Technology Center, Saiwai-cho Branch Office, Kagawa University, 2-1 Saiwai-cho, Takamatsu-shi, Kagawa, 760-8521, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Technology Center, Saiwai-cho Branch Office, Kagawa University, 2-1 Saiwai-cho, Takamatsu-shi, Kagawa, 760-8521, Japan","institution_ids":["https://openalex.org/I201933988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072143778","display_name":"Kensuke Matsumoto","orcid":"https://orcid.org/0000-0002-4839-8295"},"institutions":[{"id":"https://openalex.org/I201933988","display_name":"Kagawa University","ror":"https://ror.org/04j7mzp05","country_code":"JP","type":"education","lineage":["https://openalex.org/I201933988"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kensuke Matsumoto","raw_affiliation_strings":["Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan","institution_ids":["https://openalex.org/I201933988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056441333","display_name":"Koji Murao","orcid":"https://orcid.org/0000-0002-7335-7196"},"institutions":[{"id":"https://openalex.org/I201933988","display_name":"Kagawa University","ror":"https://ror.org/04j7mzp05","country_code":"JP","type":"education","lineage":["https://openalex.org/I201933988"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koji Murao","raw_affiliation_strings":["Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan","institution_ids":["https://openalex.org/I201933988"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109070453","display_name":"Toshihiko Ishida","orcid":null},"institutions":[{"id":"https://openalex.org/I201933988","display_name":"Kagawa University","ror":"https://ror.org/04j7mzp05","country_code":"JP","type":"education","lineage":["https://openalex.org/I201933988"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshihiko Ishida","raw_affiliation_strings":["Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan","institution_ids":["https://openalex.org/I201933988"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017566247"],"corresponding_institution_ids":["https://openalex.org/I201933988"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5609,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.67293832,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"112","last_page":"112"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3727000057697296,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3727000057697296,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.357699990272522,"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":0.1446000039577484,"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/robustness","display_name":"Robustness (evolution)","score":0.7509574890136719},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5648677349090576},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4659970998764038},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4524305462837219},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43434062600135803},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3204527795314789},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12212681770324707}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7509574890136719},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5648677349090576},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4659970998764038},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4524305462837219},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43434062600135803},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3204527795314789},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12212681770324707}],"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":"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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-112","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-112","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-112","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18294369","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18294369","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c95f4f1cdaa740afa0158aca00e7f9d4","is_oa":true,"landing_page_url":"https://doaj.org/article/c95f4f1cdaa740afa0158aca00e7f9d4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 112 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2267439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2267439","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-112","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-112","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-112","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.7300000190734863}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2051348758.pdf","grobid_xml":"https://content.openalex.org/works/W2051348758.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1965280193","https://openalex.org/W2004232360","https://openalex.org/W2050902903","https://openalex.org/W2053602505","https://openalex.org/W2054624670","https://openalex.org/W2057998009","https://openalex.org/W2058682865","https://openalex.org/W2072603644","https://openalex.org/W2085285101","https://openalex.org/W2085442947","https://openalex.org/W2094036688","https://openalex.org/W2095824228","https://openalex.org/W2099269438","https://openalex.org/W2103465619","https://openalex.org/W2104905992","https://openalex.org/W2105926960","https://openalex.org/W2106882534","https://openalex.org/W2107903949","https://openalex.org/W2110291136","https://openalex.org/W2115379981","https://openalex.org/W2135030836","https://openalex.org/W2155237411","https://openalex.org/W2158356009","https://openalex.org/W2161387979","https://openalex.org/W2166898290"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"BACKGROUND:":[0],"Detecting":[1],"conserved":[2,76],"noncoding":[3],"sequences":[4,41,153,175,188],"(CNSs)":[5],"across":[6],"species":[7],"highlights":[8],"the":[9,56,103,114,136,183,197],"functional":[10],"elements.":[11,29],"Alignment":[12],"procedures":[13],"combined":[14],"with":[15],"computational":[16],"prediction":[17],"of":[18,90,105,185,196],"transcription":[19],"factor":[20],"binding":[21],"sites":[22,117,132],"(TFBSs)":[23],"can":[24,169,202],"narrow":[25],"down":[26],"key":[27],"regulatory":[28,58,187,198],"Repeat":[30],"masking":[31],"processes":[32],"are":[33,121,193],"often":[34],"performed":[35],"before":[36],"alignment":[37,63,89],"to":[38,54,68,150,161,173],"mask":[39],"insertion":[40],"such":[42,49],"as":[43],"transposable":[44],"elements":[45],"(TEs).":[46],"However,":[47],"recently":[48],"TEs":[50,138],"have":[51],"been":[52],"reported":[53],"influence":[55],"gene":[57],"network":[59,199],"evolution.":[60,200],"Therefore,":[61],"an":[62],"approach":[64],"that":[65,98,142],"is":[66,71],"robust":[67],"TE":[69,158],"insertions":[70,151],"meaningful":[72],"for":[73,87,152],"finding":[74,186],"novel":[75],"TFBSs":[77,101],"in":[78,112,190],"TEs.":[79,106],"RESULTS:":[80],"We":[81],"constructed":[82],"a":[83,145],"web":[84],"server":[85],"'ReAlignerV'":[86],"complex":[88],"genomic":[91],"sequences.":[92],"ReAlignerV":[93,143,168,201],"returns":[94],"ladder-like":[95],"schematic":[96],"alignments":[97,111],"integrate":[99],"predicted":[100,115],"and":[102,118,140,148,165,180,206],"location":[104],"It":[107],"also":[108],"provides":[109],"pair-wise":[110],"which":[113,192],"TFBS":[116],"their":[119],"names":[120],"shown":[122],"alongside":[123],"each":[124],"sequence.":[125],"Furthermore,":[126],"we":[127],"evaluated":[128],"false":[129],"positive":[130],"aligned":[131],"by":[133],"focusing":[134],"on":[135],"species-specific":[137],"(SSTEs),":[139],"found":[141],"has":[144],"higher":[146],"specificity":[147],"robustness":[149],"having":[154],"more":[155],"than":[156],"20%":[157],"content,":[159],"compared":[160],"LAGAN,":[162],"AVID,":[163],"MAVID":[164],"BLASTZ.":[166],"CONCLUSION:":[167],"be":[170,203],"applied":[171],"successfully":[172],"TE-insertion-rich":[174],"without":[176],"prior":[177],"repeat":[178],"masking,":[179],"this":[181],"increases":[182],"chances":[184],"hidden":[189],"TEs,":[191],"important":[194],"sources":[195],"accessed":[204],"through":[205],"downloaded":[207],"from":[208],"http://genet.med.kagawa-u.ac.jp/.":[209]},"counts_by_year":[{"year":2020,"cited_by_count":11},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
