Set of rules for genomic signal downsampling

Simple item page
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorVítková, Helenacs
dc.contributor.authorVítek, Martincs
dc.contributor.authorProvazník, Valentýnacs
dc.coverage.issuep1cs
dc.coverage.volume64cs
dc.date.issued2015-06-04cs
dc.description.abstractComparison and classification of organisms based on molecular data is an important task of computational biology, since at least parts of DNA sequences for many organisms are available. Unfortunately, methods for comparison are computationally very demanding, suitable only for short sequences. In this paper, we focus on the redundancy of genetic information stored in DNA sequences. We proposed rules for downsampling of DNA signals of cumulated phase. According to the length of an original sequence, we are able to significantly reduce the amount of data with only slight loss of original information. Dyadic wavelet transform was chosen for fast downsampling with minimum influence on signal shape carrying the biological information. We proved the usability of such new short signals by measuring percentage deviation of pairs of original and downsampled signals while maintaining spectral power of signals. Minimal loss of biological information was proved by measuring the Robinson-Foulds distance between pairs of phylogenetic trees reconstructed from the original and downsampled signals. The preservation of inter-species and intra-species information makes these signals suitable for fast sequence identification as well as for more detailed phylogeny reconstruction.en
dc.description.abstractPorovnání a klasifikace organismů založená na molekulárních datech je důležitá část výpočetní biologie. V tomto článku jsme se zaměřili na redundanci genetické informace v DNA sekvencích.cs
dc.formattextcs
dc.format.extent1-7cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationCOMPUTERS IN BIOLOGY AND MEDICINE. 2015, vol. 64, issue p1, p. 1-7.en
dc.identifier.doi10.1016/j.compbiomed.2015.05.022cs
dc.identifier.issn0010-4825cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.orcid0000-0003-4562-2746cs
dc.identifier.orcid0000-0002-8059-1087cs
dc.identifier.orcid0000-0002-3422-7938cs
dc.identifier.other115093cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.researcheridD-5194-2014cs
dc.identifier.researcheridD-3351-2014cs
dc.identifier.researcheridF-4121-2012cs
dc.identifier.scopus56309904900cs
dc.identifier.scopus36521691000cs
dc.identifier.scopus35767287500cs
dc.identifier.scopus6701729526cs
dc.identifier.urihttp://hdl.handle.net/11012/69200
dc.language.isoencs
dc.publisherElseviercs
dc.relation.ispartofCOMPUTERS IN BIOLOGY AND MEDICINEcs
dc.relation.urihttp://www.sciencedirect.com/science/article/pii/S0010482515002048cs
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/0010-4825/cs
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/cs
dc.subjectGenomic signalen
dc.subjectCumulated phaseen
dc.subjectDownsamplingen
dc.subjectCompressionen
dc.subjectDWTen
dc.subjectSequence identificationen
dc.subjectPhylogenyen
dc.titleSet of rules for genomic signal downsamplingen
dc.title.alternativeSoubor pravidel pro podvzorkování genomických signálůcs
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-115093en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:40:04en
sync.item.modts2025.01.17 19:35:01en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
1s2.0S0010482515002048main.pdf
Size:
842.09 KB
Format:
Adobe Portable Document Format
Description:
1s2.0S0010482515002048main.pdf
Download
Collections
Ústav biomedicínského inženýrství