{"id":"https://openalex.org/W2150364384","doi":"https://doi.org/10.1186/1751-0473-8-6","title":"RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics","display_name":"RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics","publication_year":2013,"publication_date":"2013-02-26","ids":{"openalex":"https://openalex.org/W2150364384","doi":"https://doi.org/10.1186/1751-0473-8-6","mag":"2150364384","pmid":"https://pubmed.ncbi.nlm.nih.gov/23442262"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-8-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-6","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088741011","display_name":"Akiko Izawa","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I26120043","display_name":"Ochanomizu University","ror":"https://ror.org/03599d813","country_code":"JP","type":"education","lineage":["https://openalex.org/I26120043"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akiko Izawa","raw_affiliation_strings":["Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan. sesejun@cs.titech.ac.jp","Department of Computer Science, Ochanomizu University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan. sesejun@cs.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, Ochanomizu University, Tokyo, Japan","institution_ids":["https://openalex.org/I26120043"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022912020","display_name":"Jun Sese","orcid":"https://orcid.org/0000-0003-3495-4382"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Jun Sese","raw_affiliation_strings":["Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022912020"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":{"value":2040,"currency":"USD","value_usd":2040},"apc_paid":{"value":2040,"currency":"USD","value_usd":2040},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.09706666,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"8","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.546500027179718,"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":0.546500027179718,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.13210000097751617,"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":0.042500000447034836,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6582140922546387},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5761775374412537},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.5491172075271606},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5189452171325684},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5136324763298035},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39614322781562805},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.234317809343338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1824685037136078},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10917031764984131},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10084143280982971}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6582140922546387},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5761775374412537},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.5491172075271606},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5189452171325684},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5136324763298035},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39614322781562805},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.234317809343338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1824685037136078},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10917031764984131},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10084143280982971}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1751-0473-8-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-6","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23442262","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23442262","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2621832","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3621688","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3621688","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3621688","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":"Source Code Biol Med","raw_type":"Text"},{"id":"pmh:oai:t2r2.star.titech.ac.jp:50214712","is_oa":false,"landing_page_url":"http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100659979","pdf_url":null,"source":{"id":"https://openalex.org/S4377196385","display_name":"Tokyo Tech Research Repository (Tokyo Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114531698","host_organization_name":"Tokyo Institute of Technology","host_organization_lineage":["https://openalex.org/I114531698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-8-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-6","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-6","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5699999928474426}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2150364384.pdf","grobid_xml":"https://content.openalex.org/works/W2150364384.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1981509058","https://openalex.org/W1987301268","https://openalex.org/W2017641297","https://openalex.org/W2021341670","https://openalex.org/W2055043387","https://openalex.org/W2103441770","https://openalex.org/W2106678197","https://openalex.org/W2124985265","https://openalex.org/W2126419817","https://openalex.org/W2127640118","https://openalex.org/W2129795133","https://openalex.org/W2136145671","https://openalex.org/W2141652419","https://openalex.org/W2915985519"],"related_works":["https://openalex.org/W2353644209","https://openalex.org/W2347127313","https://openalex.org/W2348743188","https://openalex.org/W4387423451","https://openalex.org/W2902317490","https://openalex.org/W2025460258","https://openalex.org/W1741600793","https://openalex.org/W2096879929","https://openalex.org/W2593663830","https://openalex.org/W2053972265"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,163],"whole-genome":[2],"sequences":[3],"of":[4,30,50,54,71,77,87,99,106,114,142,152,168],"many":[5],"non-model":[6],"organisms":[7],"have":[8,25,36],"recently":[9],"been":[10,26],"determined.":[11],"Using":[12],"these":[13,46],"genome":[14,52,105,139],"sequences,":[15],"next-generation":[16,144],"sequencing":[17,145],"based":[18],"experiments":[19,32],"such":[20],"as":[21],"RNA-seq":[22],"and":[23,28,42,123],"ChIP-seq":[24,156],"performed":[27],"comparisons":[29,47],"the":[31,51,55,58,68,74,97,104,121,150,178],"between":[33,57,158],"related":[34],"species":[35,109,118],"provided":[37],"new":[38],"knowledge":[39],"about":[40],"evolution":[41],"biological":[43],"processes.":[44],"Although":[45],"require":[48],"transformation":[49],"coordinates":[53,76,98],"reads":[56,72,101],"species,":[59],"current":[60],"software":[61],"tools":[62],"are":[63],"not":[64],"suitable":[65],"to":[66,73,95,112],"convert":[67],"massive":[69],"numbers":[70],"corresponding":[75],"other":[78],"species'":[79],"genomes.":[80],"RESULTS:":[81],"Here,":[82],"we":[83],"introduce":[84],"a":[85,107,115,169],"set":[86],"programs,":[88],"called":[89],"REad":[90],"COordinate":[91],"Transformer":[92],"(RECOT),":[93],"created":[94],"transform":[96],"short":[100],"obtained":[102],"from":[103],"query":[108,122],"being":[110],"studied":[111],"that":[113,133],"comparison":[116],"target":[117,124],"after":[119],"aligning":[120],"gene/genome":[125],"sequences.":[126],"RECOT":[127,153],"generates":[128],"output":[129],"in":[130,154],"SAM":[131],"format":[132],"can":[134],"be":[135],"viewed":[136],"using":[137],"recent":[138],"browsers":[140],"capable":[141],"displaying":[143],"data.":[146],"CONCLUSIONS:":[147],"We":[148],"demonstrate":[149],"usefulness":[151],"comparing":[155],"results":[157,164],"two":[159],"closely-related":[160],"fruit":[161],"flies.":[162],"indicate":[165],"position":[166],"changes":[167],"transcription":[170],"factor":[171],"binding":[172,179],"site":[173],"caused":[174],"sequence":[175],"polymorphisms":[176],"at":[177],"site.":[180]},"counts_by_year":[{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
