{"id":"https://openalex.org/W2044658648","doi":"https://doi.org/10.1016/j.gpb.2012.06.007","title":"TrFAST: A Tool to Predict Signaling Pathway-Specific Transcription Factor Binding Sites","display_name":"TrFAST: A Tool to Predict Signaling Pathway-Specific Transcription Factor Binding Sites","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2044658648","doi":"https://doi.org/10.1016/j.gpb.2012.06.007","mag":"2044658648","pmid":"https://pubmed.ncbi.nlm.nih.gov/23317703"},"language":"en","primary_location":{"id":"doi:10.1016/j.gpb.2012.06.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2012.06.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.gpb.2012.06.007","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070759140","display_name":"Umair Seemab","orcid":null},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Umair Seemab","raw_affiliation_strings":["National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050950060","display_name":"Qurrat Ul Ain","orcid":"https://orcid.org/0000-0002-6891-9887"},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Qurrat ul Ain","raw_affiliation_strings":["National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047872441","display_name":"Muhammad Sulaman Nawaz","orcid":"https://orcid.org/0000-0002-5576-9007"},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Sulaman Nawaz","raw_affiliation_strings":["National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001284645","display_name":"Zafar Saeed","orcid":"https://orcid.org/0000-0002-1282-5478"},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Zafar Saeed","raw_affiliation_strings":["Department of Computer Science, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Quaid-i-Azam University , Islamabad, 44000 , Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037500655","display_name":"Sajid Rashid","orcid":"https://orcid.org/0000-0003-2122-2799"},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Sajid Rashid","raw_affiliation_strings":["National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan","institution_ids":["https://openalex.org/I12469534"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5037500655","https://openalex.org/A5070759140"],"corresponding_institution_ids":["https://openalex.org/I12469534"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.08982973,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"10","issue":"6","first_page":"354","last_page":"359"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9965999722480774,"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/dna-binding-site","display_name":"DNA binding site","score":0.7260936498641968},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6957495808601379},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6430196166038513},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5962203145027161},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4894479811191559},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4730081856250763},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4576598107814789},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4434187114238739},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44266873598098755},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.42232826352119446},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31294918060302734},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2407780885696411},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09058141708374023},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.08063298463821411}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7260936498641968},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6957495808601379},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6430196166038513},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5962203145027161},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4894479811191559},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4730081856250763},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4576598107814789},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4434187114238739},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44266873598098755},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.42232826352119446},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31294918060302734},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2407780885696411},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09058141708374023},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.08063298463821411}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051153","descriptor_name":"Wnt Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060449","descriptor_name":"Wnt Signaling Pathway","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/j.gpb.2012.06.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2012.06.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23317703","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23317703","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4016630","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054711","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/j.gpb.2012.06.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2012.06.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1539097250","display_name":null,"funder_award_id":"20-1493/R&amp","funder_id":"https://openalex.org/F4320322799","funder_display_name":"Higher Education Commission, Pakistan"},{"id":"https://openalex.org/G8292916889","display_name":null,"funder_award_id":"20-1493/R&D/09","funder_id":"https://openalex.org/F4320322799","funder_display_name":"Higher Education Commission, Pakistan"}],"funders":[{"id":"https://openalex.org/F4320322799","display_name":"Higher Education Commission, Pakistan","ror":"https://ror.org/038y3sz68"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W173128540","https://openalex.org/W1481594784","https://openalex.org/W1500827124","https://openalex.org/W1506725161","https://openalex.org/W1535438232","https://openalex.org/W1851628923","https://openalex.org/W1971430786","https://openalex.org/W1978525834","https://openalex.org/W1985924888","https://openalex.org/W1995392458","https://openalex.org/W1999177172","https://openalex.org/W2001233190","https://openalex.org/W2001770641","https://openalex.org/W2017002454","https://openalex.org/W2019621874","https://openalex.org/W2036424866","https://openalex.org/W2037821015","https://openalex.org/W2052908553","https://openalex.org/W2056050795","https://openalex.org/W2078034709","https://openalex.org/W2083992760","https://openalex.org/W2089107511","https://openalex.org/W2095193332","https://openalex.org/W2098024635","https://openalex.org/W2100847260","https://openalex.org/W2101186976","https://openalex.org/W2124008135","https://openalex.org/W2152532651","https://openalex.org/W2162558393","https://openalex.org/W2162778212","https://openalex.org/W2167728826","https://openalex.org/W2171356375","https://openalex.org/W2437224163","https://openalex.org/W2528164570","https://openalex.org/W4249058026","https://openalex.org/W4292820908","https://openalex.org/W6684306447"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2090848290","https://openalex.org/W2146393977","https://openalex.org/W2146884677"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,41,80,86,91,112,122],"the":[3,40,73,93,98,106,119,128,132,140,157,172],"development":[4],"of":[5,13,44,50,62,76,95,143,159,166,174,183,185],"high-throughput":[6],"tools":[7,108],"have":[8],"significantly":[9],"revolutionized":[10],"our":[11],"understanding":[12],"molecular":[14],"mechanisms":[15],"underlying":[16],"normal":[17],"and":[18,32,138,176],"dysfunctional":[19],"biological":[20],"processes.":[21],"Here":[22],"we":[23],"present":[24],"a":[25,113,152,178],"novel":[26],"computational":[27],"tool,":[28],"transcription":[29,45],"factor":[30,46],"search":[31],"analysis":[33,43,61,165],"tool":[34],"(TrFAST),":[35],"which":[36],"was":[37],"developed":[38],"for":[39],"silico":[42],"binding":[47,78],"sites":[48,79],"(TFBSs)":[49],"signaling":[51],"pathway-specific":[52],"TFs.":[53],"TrFAST":[54,88,116,175,189],"facilitates":[55],"searching":[56],"as":[57,59],"well":[58],"comparative":[60],"regulatory":[63,163],"motifs":[64],"through":[65],"an":[66],"exact":[67,99],"pattern":[68,100,121],"matching":[69,101],"algorithm":[70],"followed":[71],"by":[72,97],"graphical":[74],"representation":[75],"matched":[77],"multiple":[81,123,134,167],"sequences":[82,124,169],"up":[83],"to":[84,105],"50kb":[85],"length.":[87],"is":[89,190],"proficient":[90],"reducing":[92],"number":[94],"comparisons":[96],"strategy.":[102],"In":[103],"contrast":[104],"pre-existing":[107],"that":[109],"find":[110],"TFBS":[111],"single":[114],"sequence,":[115],"seeks":[117],"out":[118],"desired":[120],"simultaneously.":[125],"It":[126],"counts":[127],"GC":[129],"content":[130],"within":[131],"given":[133],"sequence":[135],"data":[136],"set":[137],"assembles":[139],"combinational":[141],"details":[142],"consensus":[144],"sequence(s)":[145],"located":[146],"at":[147,193],"these":[148],"regions,":[149],"thereby":[150],"generating":[151],"visual":[153],"display":[154],"based":[155],"on":[156],"abundance":[158],"unique":[160],"pattern.":[161],"Comparative":[162],"region":[164],"orthologous":[168],"simultaneously":[170],"enhances":[171],"features":[173],"provides":[177],"significant":[179],"insight":[180],"into":[181],"study":[182],"conservation":[184],"non-coding":[186],"cis-regulatory":[187],"elements.":[188],"freely":[191],"available":[192],"http://www.fi-pk.com/trfast.html.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
