{"id":"https://openalex.org/W2964139615","doi":"https://doi.org/10.1093/bioinformatics/btz568","title":"PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities","display_name":"PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities","publication_year":2019,"publication_date":"2019-07-16","ids":{"openalex":"https://openalex.org/W2964139615","doi":"https://doi.org/10.1093/bioinformatics/btz568","mag":"2964139615","pmid":"https://pubmed.ncbi.nlm.nih.gov/31318409"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz568","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz568","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7500089","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102978291","display_name":"Thammakorn Saethang","orcid":"https://orcid.org/0000-0002-2629-0910"},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]},{"id":"https://openalex.org/I198105771","display_name":"Kasetsart University","ror":"https://ror.org/05gzceg21","country_code":"TH","type":"education","lineage":["https://openalex.org/I198105771"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Thammakorn Saethang","raw_affiliation_strings":["Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","Department of Computer Science, Kasetsart University , Bangkok, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","institution_ids":["https://openalex.org/I158708052"]},{"raw_affiliation_string":"Department of Computer Science, Kasetsart University , Bangkok, Thailand","institution_ids":["https://openalex.org/I198105771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084578305","display_name":"Kenneth Hodge","orcid":null},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Kenneth Hodge","raw_affiliation_strings":["Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087681217","display_name":"Chin\u2010Rang Yang","orcid":"https://orcid.org/0000-0002-3445-9819"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chin-Rang Yang","raw_affiliation_strings":["Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101429222","display_name":"Yue Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Zhao","raw_affiliation_strings":["Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010221979","display_name":"Ingorn Kimkong","orcid":"https://orcid.org/0000-0002-8731-0356"},"institutions":[{"id":"https://openalex.org/I198105771","display_name":"Kasetsart University","ror":"https://ror.org/05gzceg21","country_code":"TH","type":"education","lineage":["https://openalex.org/I198105771"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Ingorn Kimkong","raw_affiliation_strings":["Department of Microbiology , Faculty of Science, Kasetsart University, Bangkok, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology , Faculty of Science, Kasetsart University, Bangkok, Thailand","institution_ids":["https://openalex.org/I198105771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029048638","display_name":"Mark A. Knepper","orcid":"https://orcid.org/0000-0002-2276-8091"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark A Knepper","raw_affiliation_strings":["Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026991644","display_name":"Trairak Pisitkun","orcid":"https://orcid.org/0000-0001-6677-2271"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]},{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["TH","US"],"is_corresponding":true,"raw_author_name":"Trairak Pisitkun","raw_affiliation_strings":["Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","institution_ids":["https://openalex.org/I158708052"]},{"raw_affiliation_string":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5026991644","https://openalex.org/A5029048638"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I158708052","https://openalex.org/I4210106489"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3607,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.77810633,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"35","issue":"24","first_page":"5313","last_page":"5314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.602400004863739,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.602400004863739,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.10440000146627426,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07180000096559525,"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/logos-bible-software","display_name":"Logos Bible Software","score":0.8338103294372559},{"id":"https://openalex.org/keywords/logo","display_name":"Logo (programming language)","score":0.740598738193512},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6335156559944153},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.6328034996986389},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6230357885360718},{"id":"https://openalex.org/keywords/sequence-logo","display_name":"Sequence logo","score":0.5044764280319214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49157556891441345},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3787081241607666},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.352819561958313},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.3377922773361206},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32784879207611084},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28006455302238464},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15090933442115784},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13159766793251038},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07575252652168274},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.06227409839630127}],"concepts":[{"id":"https://openalex.org/C150506046","wikidata":"https://www.wikidata.org/wiki/Q6667822","display_name":"Logos Bible Software","level":2,"score":0.8338103294372559},{"id":"https://openalex.org/C2778720087","wikidata":"https://www.wikidata.org/wiki/Q201436","display_name":"Logo (programming language)","level":2,"score":0.740598738193512},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6335156559944153},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.6328034996986389},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6230357885360718},{"id":"https://openalex.org/C105082737","wikidata":"https://www.wikidata.org/wiki/Q7452470","display_name":"Sequence logo","level":5,"score":0.5044764280319214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49157556891441345},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3787081241607666},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.352819561958313},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3377922773361206},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32784879207611084},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28006455302238464},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15090933442115784},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13159766793251038},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07575252652168274},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.06227409839630127},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz568","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz568","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31318409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31318409","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7500089","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7500089","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7500089","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7500089","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G4530535874","display_name":null,"funder_award_id":"HL-006129","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6123656145","display_name":null,"funder_award_id":"RSA6280026","funder_id":"https://openalex.org/F4320322614","funder_display_name":"Thailand Research Fund"},{"id":"https://openalex.org/G8123537306","display_name":null,"funder_award_id":"HL-001285","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320321557","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58"},{"id":"https://openalex.org/F4320322614","display_name":"Thailand Research Fund","ror":"https://ror.org/03gd1bh37"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1966223981","https://openalex.org/W1985138165","https://openalex.org/W1996310767","https://openalex.org/W2043274355","https://openalex.org/W2075840515","https://openalex.org/W2076455712","https://openalex.org/W2080600617","https://openalex.org/W2085037886","https://openalex.org/W2147054306","https://openalex.org/W2172609270","https://openalex.org/W2762504941"],"related_works":["https://openalex.org/W2946658881","https://openalex.org/W2112896459","https://openalex.org/W3127211284","https://openalex.org/W2026754580","https://openalex.org/W3198749917","https://openalex.org/W2085407156","https://openalex.org/W2098050557","https://openalex.org/W654432377","https://openalex.org/W1993445589","https://openalex.org/W2990113118"],"abstract_inverted_index":{"SUMMARY:":[0],"Identification":[1],"of":[2,16,47,57,69,77,89,97,136],"the":[3,64,81,95,98,106],"amino-acid":[4,145],"motifs":[5,26,71],"in":[6,19],"proteins":[7],"that":[8,34,87,111,133],"are":[9,172],"targeted":[10,25,70],"for":[11,123],"post-translational":[12],"modifications":[13],"(PTMs)":[14],"is":[15,160],"great":[17],"importance":[18],"understanding":[20],"regulatory":[21],"networks.":[22],"Information":[23],"about":[24],"can":[27],"be":[28],"derived":[29],"from":[30,150],"mass":[31],"spectrometry":[32],"data":[33,49,152,171],"identify":[35],"peptides":[36],"containing":[37],"specific":[38],"PTMs":[39],"such":[40,113],"as":[41],"phosphorylation,":[42],"ubiquitylation":[43],"and":[44,59,100,115],"acetylation.":[45],"Comparison":[46],"input":[48],"against":[50],"a":[51,73,129],"standardized":[52],"'background'":[53],"set":[54],"allows":[55],"identification":[56],"over-":[58,114],"under-represented":[60,116],"amino":[61,78,90,117,138],"acids":[62,79,91,118],"surrounding":[63,80],"modified":[65,82,107],"site.":[66,108],"Conventionally,":[67],"calculation":[68],"assumes":[72],"random":[74],"background":[75],"distribution":[76],"position.":[83],"However,":[84],"we":[85,127],"show":[86],"probabilities":[88],"depend":[92],"on":[93,143],"(i)":[94],"type":[96],"modification":[99],"(ii)":[101],"their":[102],"positions":[103],"relative":[104],"to":[105],"Thus,":[109],"software":[110],"identifies":[112],"should":[119],"make":[120],"appropriate":[121],"adjustments":[122],"these":[124,137],"effects.":[125],"Here":[126],"present":[128],"new":[130],"program,":[131],"PTM-Logo,":[132],"generates":[134],"representations":[135],"acid":[139],"preferences":[140],"('logos')":[141],"based":[142],"position-specific":[144],"probability":[146],"backgrounds":[147],"calculated":[148],"either":[149],"user-input":[151],"or":[153,166],"curated":[154],"databases.":[155],"AVAILABILITY":[156],"AND":[157],"IMPLEMENTATION:":[158],"PTM-Logo":[159],"freely":[161],"available":[162,173],"online":[163],"at":[164,174],"http://sysbio.chula.ac.th/PTMLogo/":[165],"https://hpcwebapps.cit.nih.gov/PTMLogo/.":[167],"SUPPLEMENTARY":[168],"INFORMATION:":[169],"Supplementary":[170],"Bioinformatics":[175],"online.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
