Abstract:
BACKGROUND:A cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score function for high-resolution spectra by improving the preprocessing step of the tandem mass spectra. However, despite the development of the HiXCorr algorithm, the score function is still slow because candidate peptides increase when post-translational modifications (PTMs) are considered in the search. RESULTS:We used a graphics processing unit (GPU) to develop the accelerating score function derived by combining Tide's XCorr score function and the HiXCorr algorithm. Our method is 2.7 and 5.8 times faster than the original Tide and Tide-Hi, respectively, for 50 Da precursor tolerance. Our GPU-based method produced identical scores as did the CPU-based Tide and Tide-Hi. CONCLUSION:We propose the accelerating score function to search modifications using a single GPU. The software is available at https://github.com/Tide-for-PTM-search/Tide-for-PTM-search .
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Kim H,Han S,Um JH,Park Kdoi
10.1186/s12859-018-2559-6subject
Has Abstractpub_date
2018-12-12 00:00:00pages
480issue
1issn
1471-2105pii
10.1186/s12859-018-2559-6journal_volume
19pub_type
杂志文章abstract:BACKGROUND:Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detec...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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abstract:BACKGROUND:The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially ...
journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2013-11-14 00:00:00
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journal_title:BMC bioinformatics
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-10-29 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2020-03-11 00:00:00
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pub_type: 杂志文章
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更新日期:2015-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
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更新日期:2009-11-10 00:00:00
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pub_type: 杂志文章
doi:10.1186/s12859-019-2964-5
更新日期:2019-06-28 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S12-S7
更新日期:2008-12-12 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-74
更新日期:2005-03-24 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2018-11-22 00:00:00
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journal_title:BMC bioinformatics
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更新日期:2013-08-22 00:00:00
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更新日期:2011-10-05 00:00:00
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更新日期:2008-11-27 00:00:00
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更新日期:2011-02-15 00:00:00
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更新日期:2020-08-21 00:00:00
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更新日期:2009-03-06 00:00:00
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