download0 view389
twitter facebook

공공누리This item is licensed Korea Open Government License

dc.contributor.author
김현우
dc.contributor.author
박희진
dc.contributor.author
이상정
dc.date.accessioned
2022-03-30T01:32:21Z
dc.date.available
2022-03-30T01:32:21Z
dc.date.issued
2019-08-23
dc.identifier.issn
1471-2105
dc.identifier.uri
https://repository.kisti.re.kr/handle/10580/16587
dc.description.abstract
Background: One of the most important steps in peptide identification is to estimate the false discovery rate (FDR). The most commonly used method for estimating FDR is the target-decoy search strategy (TDS). While this method is simple and effective, it is time/space-inefficient because it searches a database that is twice as large as the original protein database. This inefficiency problem becomes more evident as protein databases get bigger and bigger. We propose a target-small decoy search strategy and present a rigorous verification that it reduces the database size and search time while retaining the accuracy of target-decoy search strategy (TDS).

Results: We show that peptide spectrum matches (PSMs) obtained at 1% FDR in TDS overlap ~ 99% with those in our method. (Considering that 1% FDR is used, 99% overlap means our method is very accurate.) Moreover, our method is more time/space-efficient than TDS. The search time of our method is reduced to only 1/4 of that of TDS when UniProt and its 1/8 decoy database are used.

Conclusions: We demonstrate that our method is almost as accurate as TDS and more time/space-efficient than TDS. Since the efficiency of our method is more evident as the database size increases, our method is expected to be useful for identifying peptides in proteogenomics databases constructed from inflated databases using genomic data.
dc.language.iso
eng
dc.publisher
BioMed Central
dc.relation.ispartofseries
BMC bioinformatics;
dc.title
Target-small decoy search strategy for false discovery rate estimation
dc.identifier.doi
10.1186/s12859-019-3034-8
dc.citation.number
1
dc.citation.volume
20
dc.contributor.approver
KOAR, ADMIN
dc.date.dateaccepted
2022-03-30T01:32:21Z
dc.date.datesubmitted
2022-03-30T01:32:21Z
dc.identifier.bibliographicCitation
vol. 20, no. 1
dc.identifier.url
https://scienceon.kisti.re.kr/srch/selectPORSrchArticle.do?cn=NART108698358
dc.subject.keyword
Target-decoy search
dc.subject.keyword
Target-small decoy search
dc.subject.keyword
False discovery rate
Appears in Collections:
7. KISTI 연구성과 > 학술지 발표논문
Files in This Item:
There are no files associated with this item.

Browse