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dc.contributor.author박희진-
dc.date.accessioned2018-03-26T07:27:57Z-
dc.date.available2018-03-26T07:27:57Z-
dc.date.issued2014-12-
dc.identifier.citationPROTEOMICS, 14(23-24), p.2742-2749en_US
dc.identifier.issn1615-9853-
dc.identifier.issn1615-9861-
dc.identifier.urihttps://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201400225-
dc.identifier.urihttp://hdl.handle.net/20.500.11754/52537-
dc.description.abstractIn proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variantssingle nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches.en_US
dc.description.sponsorshipThis research was supported by the Proteogenomics Research Program (NRF-2012M3A9B9036675, NRF-2012M3A9B9036676) through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning. Institute for Basic Science (CA1308) and NRF programs (NRF-2012M3A9D1054452, NRF-2014M3C7A1046047) were also acknowledged.en_US
dc.language.isoenen_US
dc.publisherWILEY-BLACKWELLen_US
dc.subjectBioinformaticsen_US
dc.subjectEarly onset gastric canceren_US
dc.subjectPeptide identificationen_US
dc.subjectProteogenomicsen_US
dc.subjectSequence databaseen_US
dc.titleCompact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analysesen_US
dc.typeArticleen_US
dc.relation.volume14-
dc.identifier.doi10.1002/pmic.201400225-
dc.relation.page2742-2749-
dc.relation.journalPROTEOMICS-
dc.contributor.googleauthorPark, Heejin-
dc.contributor.googleauthorBae, Junwoo-
dc.contributor.googleauthorKim, Hyunwoo-
dc.contributor.googleauthorKim, Sangok-
dc.contributor.googleauthorKim, Hokeun-
dc.contributor.googleauthorMun, Dong-Gi-
dc.contributor.googleauthorJoh, Yoonsung-
dc.contributor.googleauthorLee, Wonyeop-
dc.contributor.googleauthorChae, Sehyun-
dc.contributor.googleauthorLee, Sanghyuk-
dc.relation.code2014038202-
dc.sector.campusS-
dc.sector.daehakCOLLEGE OF ENGINEERING[S]-
dc.sector.departmentDEPARTMENT OF COMPUTER SCIENCE-
dc.identifier.pidhjpark-
Appears in Collections:
COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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