{"id":"https://openalex.org/W2155333552","doi":"https://doi.org/10.1186/1471-2105-7-390","title":"PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data","display_name":"PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data","publication_year":2006,"publication_date":"2006-08-25","ids":{"openalex":"https://openalex.org/W2155333552","doi":"https://doi.org/10.1186/1471-2105-7-390","mag":"2155333552","pmid":"https://pubmed.ncbi.nlm.nih.gov/16934139"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-390","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-390","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-390","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/10.1186/1471-2105-7-390","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108510267","display_name":"Kuo Ping Chiu","orcid":null},"institutions":[{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Kuo Ping Chiu","raw_affiliation_strings":["Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, 138672, Singapore. chiukp@gis.a-star.edu.sg","Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, 138672, Singapore. chiukp@gis.a-star.edu.sg","institution_ids":["https://openalex.org/I66068411"]},{"raw_affiliation_string":"Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061824149","display_name":"Chee\u2010Hong Wong","orcid":"https://orcid.org/0000-0003-4546-4979"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee-Hong Wong","raw_affiliation_strings":["Bioinformatics Institute, 30 Biopolis Street, Matrix, #08-01, 138671, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, 30 Biopolis Street, Matrix, #08-01, 138671, Singapore","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028189129","display_name":"Qiongyu Chen","orcid":"https://orcid.org/0000-0001-5283-5614"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Qiongyu Chen","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113838480","display_name":"Pramila Ariyaratne","orcid":null},"institutions":[{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Pramila Ariyaratne","raw_affiliation_strings":["Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110260103","display_name":"Hong Ooi","orcid":null},"institutions":[{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hong Sain Ooi","raw_affiliation_strings":["Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025894522","display_name":"Chia\u2010Lin Wei","orcid":"https://orcid.org/0000-0001-6820-0461"},"institutions":[{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chia-Lin Wei","raw_affiliation_strings":["Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012563463","display_name":"Wing\u2010Kin Sung","orcid":"https://orcid.org/0000-0001-7806-7086"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Wing-Kin Ken Sung","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore","Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028790437","display_name":"Yijun Ruan","orcid":"https://orcid.org/0000-0001-5881-569X"},"institutions":[{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yijun Ruan","raw_affiliation_strings":["Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.8638,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.90702357,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"7","issue":"1","first_page":"390","last_page":"390"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3066999912261963,"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":0.3066999912261963,"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/T10885","display_name":"Gene expression and cancer classification","score":0.17180000245571136,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.1687999963760376,"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/computer-science","display_name":"Computer science","score":0.6587038040161133},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5495287179946899},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5018362998962402},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.474173903465271},{"id":"https://openalex.org/keywords/extractor","display_name":"Extractor","score":0.4185481369495392},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3976905345916748},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3550368845462799},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19315007328987122},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11833414435386658}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6587038040161133},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5495287179946899},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5018362998962402},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.474173903465271},{"id":"https://openalex.org/C117978034","wikidata":"https://www.wikidata.org/wiki/Q5422192","display_name":"Extractor","level":2,"score":0.4185481369495392},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3976905345916748},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3550368845462799},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19315007328987122},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11833414435386658},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C21880701","wikidata":"https://www.wikidata.org/wiki/Q2144042","display_name":"Process engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"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":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-390","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-390","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-390","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:16934139","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16934139","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:scholarbank.nus.edu.sg:10635/38887","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/38887","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:0260fdfca5624f5aac68132547d4b4d7","is_oa":true,"landing_page_url":"https://doaj.org/article/0260fdfca5624f5aac68132547d4b4d7","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 7, Iss 1, p 390 (2006)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1564156","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-390","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:10.1186/1471-2105-7-390","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-390","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-390","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320696","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155333552.pdf","grobid_xml":"https://content.openalex.org/works/W2155333552.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W2000013297","https://openalex.org/W2002982210","https://openalex.org/W2010888033","https://openalex.org/W2030817277","https://openalex.org/W2069047984","https://openalex.org/W2099468911","https://openalex.org/W2110015307","https://openalex.org/W2114703458","https://openalex.org/W2125558666","https://openalex.org/W2151238743","https://openalex.org/W2151587693","https://openalex.org/W2154628824","https://openalex.org/W2159227212","https://openalex.org/W2171407623","https://openalex.org/W2187417714","https://openalex.org/W2247766769","https://openalex.org/W2573814393","https://openalex.org/W4213387068","https://openalex.org/W4249877820"],"related_works":["https://openalex.org/W2921363728","https://openalex.org/W2279684808","https://openalex.org/W3217304749","https://openalex.org/W2066142713","https://openalex.org/W2894932706","https://openalex.org/W2767606877","https://openalex.org/W2582968398","https://openalex.org/W4223446368","https://openalex.org/W4232517363","https://openalex.org/W3214020344"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,83],"recently":[2],"developed":[3],"the":[4,64,100,115,121,131,139,143,157,198],"Paired":[5],"End":[6],"diTag":[7],"(PET)":[8],"strategy":[9],"for":[10,118,124,134,147,258,264],"efficient":[11,172],"characterization":[12],"of":[13,22,35,63,112,127,152,159,190,249],"mammalian":[14],"transcriptomes":[15],"and":[16,47,59,96,142,171,177,225,234,240,262],"genomes.":[17],"The":[18,103,150,222,252],"paired":[19],"end":[20],"nature":[21],"short":[23],"PET":[24,67,72,76,94,119,128,136,162,175,192,238],"sequences":[25,68,95,137,176,193],"derived":[26],"from":[27,43,70,180,217],"long":[28],"DNA":[29],"fragments":[30],"raised":[31],"a":[32,108,202],"new":[33],"set":[34],"bioinformatics":[36],"challenges,":[37],"including":[38],"how":[39],"to":[40,53,91,99,197,212,219,244],"extract":[41],"PETs":[42,52,216],"raw":[44],"sequence":[45,129],"reads,":[46],"correctly":[48],"yet":[49],"efficiently":[50],"map":[51,97],"reference":[54],"genome":[55,101,140,199],"sequences.":[56,102,163,200,251],"To":[57],"accommodate":[58,245],"streamline":[60],"data":[61,77,148,259,266],"analysis":[62],"large":[65,181],"volume":[66,182],"generated":[69],"each":[71],"experiment,":[73],"an":[74,85,232],"automated":[75],"process":[78,93,213],"pipeline":[79],"is":[80,169,231],"desirable.":[81],"RESULTS:":[82],"designed":[84],"integrated":[86],"computation":[87],"program":[88],"package,":[89],"PET-Tool,":[90],"automatically":[92],"them":[98],"Tool":[104,253],"was":[105,154,165],"implemented":[106],"as":[107],"web-based":[109],"application":[110],"composed":[111],"four":[113],"modules:":[114],"Extractor":[116],"module":[117,123,133,146],"extraction;":[120],"Examiner":[122],"analytic":[125],"evaluation":[126],"quality;":[130],"Mapper":[132],"locating":[135],"in":[138,173,237],"sequences;":[141],"Project":[144],"Manager":[145],"organization.":[149],"performance":[151],"PET-Tool":[153,168,230],"evaluated":[155],"through":[156],"analyses":[158,248],"2.7":[160],"million":[161,215],"It":[164],"demonstrated":[166],"that":[167,229],"accurate":[170],"extracting":[174],"removing":[178],"artifacts":[179],"dataset.":[183],"Using":[184],"optimized":[185],"mapping":[186],"criteria,":[187],"over":[188],"70%":[189],"quality":[191,260],"were":[194],"mapped":[195],"specifically":[196],"With":[201],"2.4":[203],"GHz":[204],"LINUX":[205],"machine,":[206],"it":[207],"takes":[208],"approximately":[209],"six":[210],"hours":[211],"one":[214],"extraction":[218],"mapping.":[220],"CONCLUSION:":[221],"speed,":[223],"accuracy,":[224],"comprehensiveness":[226],"have":[227],"proved":[228],"important":[233],"useful":[235],"component":[236],"experiments,":[239],"can":[241],"be":[242],"extended":[243],"other":[246],"related":[247],"paired-end":[250],"also":[254],"provides":[255],"user-friendly":[256],"functions":[257],"check":[261],"system":[263],"multi-layer":[265],"management.":[267]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}