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Search of periodicities in primary structure of biopolymers: a general Fourier approach
1996
Bioinformatics
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Another fruitful technical improvement is the closing of the sequence in the ring with further scanning of the ring length, which allows the study of periods of the order of the sequence length. ...
An algorithm to compute Fourier spectrum power allows detection of vague periods in sequences containing strong repeats. ...
Moscow, Russia E-mail:makeev@imb. imb.ac.ru A variety of approaches for searching for periodical patterns in biological sequences can be reduced to two basic methods, namely Fourier analysis and the study ...
doi:10.1093/bioinformatics/12.1.49
fatcat:n6h34tzgdne6jdqimxgfnvzqdy
Fast search of locally repetitive elements based on auto-correlation property in genome
2013
13th IEEE International Conference on BioInformatics and BioEngineering
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The performance of our proposed self autocorrelation based method will be compared with that of conventional scheme for the human chromosome sequence. ...
In this paper, we propose an autocorrelation based method to arrange the repetitive elements which demonstrate a major part of the genomic sequences. ...
The analysis using various mathematical methods was done for the genomic sequences. A frequency-domain analysis for biomolecular sequences used discrete complex value to analyze DNA sequences [7] . ...
doi:10.1109/bibe.2013.6701582
dblp:conf/bibe/ShinCKC13
fatcat:msakotk7cbhepbvfifgn2bvveq
DNA sequence comparison based on Tabular Representation
2005
INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY
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DNA sequence comparison remains as one of the critical steps in the analysis of phylogenetic relationships between species. ...
We have been developing tools for the analysis of protein The method is very simple and fast, and it can be used to analyze both short and long DNA sequences. ...
The FASTP program can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. ...
doi:10.24297/ijct.v4i1c.3121
fatcat:fzhoydpmgjbfnon2vvxripgwya
Periodicity of DNA in exons
2004
BMC Molecular Biology
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It was also found that DNA periodicity disappears in the simulated sequences, when the frequencies of codons become equal. ...
The periodic pattern of DNA in exons is a known phenomenon. ...
Unfortunately, the methods discussed here being very effective in quantifying DNA periodicity in a set of many sequences, are not sensitive enough for a single sequence. ...
doi:10.1186/1471-2199-5-12
pmid:15315715
pmcid:PMC516030
fatcat:aq772mqadvfirpdpkzup6k2lr4
Macromolecular sequence analysis using multiwindow Gabor representations
2008
Signal Processing
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This paper presents a technique for analysis, and comparison of DNA and protein sequences. ...
We use local periodicities to compare sequences and develop techniques that can compare the similarity between sequences in the combined space. ...
We have compared our method with the methods of [32, 2] for DNA sequences, and with those presented in [6] for protein sequences. ...
doi:10.1016/j.sigpro.2007.10.011
fatcat:kvto4mlegjbjnpzoi57wxuu3ra
Enlarged Similarity of Nucleic Acid Sequences
1996
DNA Research
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The method of mutual information calculation is developed considering the correlation of bases in compared sequences. ...
The definitions of correlated similarity and evolution similarity between compared sequences are given. Results of the use of enlarged similarity approach for DNA sequences analysis are discussed. ...
The methods of DNA sequence analysis presented in this paper were realized with Fortran programs. ...
doi:10.1093/dnares/3.3.157
pmid:8905233
fatcat:g7nmug7esjhp3mq3stnvilqai4
28 GBshape: a genome browser database for DNA shape annotations
2015
Journal of Biomolecular Structure and Dynamics
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ACKNOWLEDGEMENTS The authors thank Iris Dror for her initial work on the TSS analysis and valuable comments on the manuscript, and Luigi Manna for the setup and maintenance of the Rohs lab servers and ...
Analysis of the other DNA shape features Roll, HelT and ProT further confirmed the shared 10-bp periodicity as well as distinctions in DNA shape between nucleosome-bound sequences in these genomes ( Figure ...
Another application for DNA shape analysis would be in the functional evaluation of genetic variation, which is commonly described in terms of nucleotide sequence (12, 13) . ...
doi:10.1080/07391102.2015.1032568
fatcat:xg5grhat6ngxvmlkuugfvii3bq
An Efficient Analysis Technique For Dna Sequences Using Multiwindow Gabor Representations
2005
Zenodo
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Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005 ...
case of changes also helps in examining the periodicity properties in DNA sequences. ...
This would therefore, compare only corresponding high value coefficients in the two sequences and reduce the computational time for searching. ...
doi:10.5281/zenodo.39212
fatcat:tbnd3fykejci3enm622vlvbj7m
Identification of Protein Coding Regions Using the Modified Gabor-Wavelet Transform
2008
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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An important topic in genomic sequence analysis is the identification of protein coding regions. ...
In this context, several coding DNA model-independent methods based on the occurrence of specific patterns of nucleotides at coding regions have been proposed. ...
The work of J.P. Mena-Chalco was supported by CAPES. ...
doi:10.1109/tcbb.2007.70259
pmid:18451429
fatcat:4b5olitfd5allfsn33jlxtcgia
LEPSCAN--a web server for searching latent periodicity in DNA sequences
2011
Briefings in Bioinformatics
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This method allows searching latent periodicity in presence of insertions and deletions. ...
A web server for searching latent periodicity based on the method of modified profile analysis has been developed. ...
Key Points LEPSCAN is a web server for searching latent periodicity based on the method of MPA. This method allows searching latent periodicity in presence of insertions and deletions. ...
doi:10.1093/bib/bbr044
pmid:22396486
fatcat:6xqduvkafnhohdunh3sfuwczma
Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes
2006
DNA Research
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We used the other new method developed by us-Modified Profile Analysis-to reveal more periodic sequences in the presence of indels using the classes obtained. ...
We used the method of Information Decomposition developed by us to identify the latent dinucleotide periodicity regions in bacterial genomes. ...
Acknowledgements: The work presented in this paper was supported in part by the Russian Federal Ministry for Science and Education in the context of the 'System Biology' project (2005)(2006). ...
doi:10.1093/dnares/dsl004
pmid:16980713
fatcat:dxwjvgcgb5aenbydwgxrdkqnxe
HeteroGenome: database of genome periodicity
2014
Database: The Journal of Biological Databases and Curation
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We obtained data with the aid of a spectral-statistical approach to search for reliable latent periodicity regions (with periods up to 2000 bp) in DNA sequences. ...
Analysis of the quantitative and qualitative content of located periodicity regions on all chromosomes of the analyzed organisms revealed dominant characteristic types of periodicity in the genomes. ...
Conflict of interest. None declared. ...
doi:10.1093/database/bau040
pmid:24857969
pmcid:PMC4038257
fatcat:2zibvy2erngmzgnj4cx2zk6gdu
The Distribution of Eigenvalues of Covariance Matrices of Residuals in Analysis of Variance
1970
Journal of Research of the National Bureau of Standards Section B Mathematical Sciences
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In this paper, we proposed new algorithm for image similarity to compare among variance covariance matrix eigenvalues images of Fast Fourier Transform (FFT) for numerical values representation of DNA sequences ...
It should be noted that it is the first time that the variance covariance matrix eigenvalues of Fast Fourier Transform (FFT) for numerical values representation of DNA sequences, is used in an analysis ...
The proposed method make a quantitative analysis and compute the defined texture features of a DNA sequence. ...
doi:10.6028/jres.074b.014
fatcat:enovknjanfc2plgeh5nrpods4u
An agent-based system for re-annotation of genomes
2005
Genetics and Molecular Research
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The results reported by the system identify most of new features present in the re-annotated versions of these genomes. ...
These tasks involve BLAST searches on biological databases (GenBank) and the use of detection tools (Genemark and Glimmer) to identify new open reading frames. ...
This re-annotation process combined sequence similarity searches with statistical analysis of the DNA sequences, using the Genemark program. ...
pmid:16342042
fatcat:xr4twzgakjcnlayfnmkmmu536e
Application of the Burrows-Wheeler Transform for Searching for Approximate Tandem Repeats
[chapter]
2012
Lecture Notes in Computer Science
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Both TRs and ATRs are used in forensic analysis, DNA mapping, testing for inherited diseases and many evolutionary studies. ...
This paper presents our method for searching for ATRs defined on the basis of the model of substitution mutations and its comparison to two other tools. ...
TRs belong to the most important loci in genomes due to their abundance in DNA sequences and to their role both in evolution and in molecular mechanism of functioning of organisms. ...
doi:10.1007/978-3-642-34123-6_23
fatcat:2fsr34gpija5dhrsf6hb7o3u6q
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