{"id":"https://openalex.org/W2429135500","doi":"https://doi.org/10.1186/s12859-016-1133-3","title":"PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq","display_name":"PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq","publication_year":2016,"publication_date":"2016-06-17","ids":{"openalex":"https://openalex.org/W2429135500","doi":"https://doi.org/10.1186/s12859-016-1133-3","mag":"2429135500","pmid":"https://pubmed.ncbi.nlm.nih.gov/27316337"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1133-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1133-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1133-3","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/track/pdf/10.1186/s12859-016-1133-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011332528","display_name":"Bo Wen","orcid":"https://orcid.org/0000-0003-2261-3150"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Wen","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072996397","display_name":"Shaohang Xu","orcid":"https://orcid.org/0000-0002-6106-031X"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaohang Xu","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009012195","display_name":"Ruo Zhou","orcid":"https://orcid.org/0000-0002-3747-6147"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruo Zhou","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100389664","display_name":"Bing Zhang","orcid":"https://orcid.org/0000-0001-8676-2425"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bing Zhang","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100411595","display_name":"Xiaojing Wang","orcid":"https://orcid.org/0000-0002-4049-8822"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaojing Wang","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100352324","display_name":"Xin Liu","orcid":"https://orcid.org/0000-0003-3256-2940"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Liu","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100451926","display_name":"Xun Xu","orcid":"https://orcid.org/0000-0002-5338-5173"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xun Xu","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100390227","display_name":"Siqi Liu","orcid":"https://orcid.org/0000-0001-9744-3681"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Siqi Liu","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China. siqiliu@genomics.cn","Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. siqiliu@genomics.cn","Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China. siqiliu@genomics.cn","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. siqiliu@genomics.cn","institution_ids":["https://openalex.org/I2801577699"]},{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China","institution_ids":["https://openalex.org/I2801577699","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100390227"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I19820366","https://openalex.org/I2801577699"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.0405,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.95479212,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"244","last_page":"244"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9350000023841858,"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":0.9350000023841858,"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/T11561","display_name":"Protein Hydrolysis and Bioactive Peptides","score":0.007799999788403511,"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":0.005400000140070915,"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/database","display_name":"Database","score":0.7083215117454529},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.5978649258613586},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5573908090591431},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5561606287956238},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5497744679450989},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.4702804386615753},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4519793391227722},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.43982255458831787},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3670511543750763},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26013773679733276},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23519879579544067},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16231560707092285},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1172364354133606},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09463852643966675}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.7083215117454529},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.5978649258613586},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5573908090591431},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5561606287956238},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5497744679450989},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.4702804386615753},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4519793391227722},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.43982255458831787},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3670511543750763},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26013773679733276},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23519879579544067},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16231560707092285},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1172364354133606},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09463852643966675},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-016-1133-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1133-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1133-3","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:27316337","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27316337","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:pubmedcentral.nih.gov:4912784","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4912784","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1133-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1133-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1133-3","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":[{"id":"https://openalex.org/G5260298421","display_name":null,"funder_award_id":"2012AA020202","funder_id":"https://openalex.org/F4320335773","funder_display_name":"National High-tech Research and Development Program"}],"funders":[{"id":"https://openalex.org/F4320335773","display_name":"National High-tech Research and Development Program","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2429135500.pdf","grobid_xml":"https://content.openalex.org/works/W2429135500.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1581343682","https://openalex.org/W1960104152","https://openalex.org/W1963696479","https://openalex.org/W1981593008","https://openalex.org/W2015556811","https://openalex.org/W2017066391","https://openalex.org/W2028673251","https://openalex.org/W2030498712","https://openalex.org/W2034969265","https://openalex.org/W2037744323","https://openalex.org/W2042160423","https://openalex.org/W2042228684","https://openalex.org/W2047275456","https://openalex.org/W2052775071","https://openalex.org/W2053573662","https://openalex.org/W2079187939","https://openalex.org/W2092760343","https://openalex.org/W2094375432","https://openalex.org/W2097065948","https://openalex.org/W2104956500","https://openalex.org/W2108234281","https://openalex.org/W2108374985","https://openalex.org/W2111846704","https://openalex.org/W2113620105","https://openalex.org/W2116106861","https://openalex.org/W2119180969","https://openalex.org/W2122532582","https://openalex.org/W2126362155","https://openalex.org/W2126419817","https://openalex.org/W2128316695","https://openalex.org/W2129272652","https://openalex.org/W2130706354","https://openalex.org/W2139561888","https://openalex.org/W2140163842","https://openalex.org/W2141458291","https://openalex.org/W2161811833","https://openalex.org/W2317664229","https://openalex.org/W2605068739","https://openalex.org/W4210290733","https://openalex.org/W4212920271"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W2140163842","https://openalex.org/W2982252354","https://openalex.org/W2154126264"],"abstract_inverted_index":{"BACKGROUND:":[0],"Peptide":[1],"identification":[2,65],"based":[3,127],"upon":[4],"mass":[5,16,112],"spectrometry":[6,113],"(MS)":[7],"is":[8,56,89,193],"generally":[9],"achieved":[10],"by":[11,231],"comparison":[12],"of":[13,53,66,71,123,156,211,227],"the":[14,19,51,64,85,110,154,200,233],"experimental":[15],"spectra":[17],"with":[18,61,84,94,131,149],"theoretically":[20],"digested":[21],"peptides":[22,143,230],"derived":[23,237],"from":[24,42,117,196,238],"a":[25,43,72,100,134,150,157],"reference":[26,44,135],"protein":[27,37,48,87,125,235],"database.":[28,45],"Obviously,":[29],"this":[30],"strategy":[31],"could":[32],"not":[33],"identify":[34,141,164],"peptide":[35,82],"and":[36,62,121,144,186,199,217,222],"sequences":[38],"that":[39,105],"are":[40,203],"absent":[41],"A":[46,92],"customized":[47,86,124,234],"database":[49,236],"on":[50,128],"basis":[52,155],"RNA-Seq":[54,129,239],"data":[55,115,130],"thus":[57],"proposed":[58],"to":[59,109,163,224],"assist":[60],"improve":[63],"novel":[67,81,142,169,188,229],"peptides.":[68,190],"Correspondingly,":[69],"development":[70],"comprehensive":[73],"pipeline,":[74],"which":[75],"provides":[76],"an":[77,95,146],"end-to-end":[78],"solution":[79],"for":[80],"detection":[83],"database,":[88],"necessary.":[90],"RESULTS:":[91],"pipeline":[93,210],"R":[96],"package,":[97],"assigned":[98],"as":[99],"PGA":[101,139,160],"utility,":[102],"was":[103,161,219],"developed":[104,221],"enables":[106],"automated":[107],"treatment":[108],"tandem":[111],"(MS/MS)":[114],"acquired":[116],"different":[118],"MS":[119],"platforms":[120],"construction":[122],"databases":[126],"or":[132],"without":[133],"genome":[136],"guide.":[137],"Hence,":[138],"can":[140],"generate":[145],"HTML-based":[147],"report":[148],"visualized":[151],"interface.":[152],"On":[153],"published":[158],"dataset,":[159],"employed":[162],"peptides,":[165,170,178,181,185],"resulting":[166],"in":[167],"636":[168],"including":[171],"510":[172],"single":[173],"amino":[174],"acid":[175],"polymorphism":[176],"(SAP)":[177],"2":[179],"INDEL":[180],"49":[182],"splice":[183],"junction":[184],"75":[187],"transcript-derived":[189],"The":[191,209],"software":[192],"freely":[194],"available":[195,204],"http://bioconductor.org/packages/PGA/":[197],",":[198],"example":[201],"reports":[202],"at":[205,214],"http://wenbostar.github.io/PGA/":[206],".":[207],"CONCLUSIONS:":[208],"PGA,":[212],"aimed":[213],"being":[215],"platform-independent":[216],"easy-to-use,":[218],"successfully":[220],"shown":[223],"be":[225],"capable":[226],"identifying":[228],"searching":[232],"data.":[240]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}