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Search of periodicities in primary structure of biopolymers: a general Fourier approach

V.Ju. Makeev, V.G. Tumanyan
1996 Bioinformatics  
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

Kyung-Seop Shin, Byung-Chang Chung, Woo-Chan Kim, Dong-Ho Cho
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
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

Archana Verma, Mr. R.K.Bharti, Prof. R.K. Singh
2005 INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY  
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

Stephen T Eskesen, Frank N Eskesen, Brian Kinghorn, Anatoly Ruvinsky
2004 BMC Molecular Biology  
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

Nagesh K. Subbanna, Yehoshua Y. Zeevi
2008 Signal Processing  
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

E. V. Korotkov, M. A. Korotkova
1996 DNA Research  
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

Tsu-Pei Chiu, Lin Yang, Tianyin Zhou, Bradley J. Main, Stephen C.J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs
2015 Journal of Biomolecular Structure and Dynamics  
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

Nagesh Subbanna, Y.Y. Zeevi
2005 Zenodo  
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

J.P. Mena-Chalco, H. Carrer, Y. Zana, R.M. Cesar
2008 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

A. Shelenkov, E. Korotkov
2011 Briefings in Bioinformatics  
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

Andrew Shelenkov, Konstantin Skryabin, Eugene Korotkov
2006 DNA Research  
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

M. Chaley, V. Kutyrkin, G. Tulbasheva, E. Teplukhina, N. Nazipova
2014 Database: The Journal of Biological Databases and Curation  
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

John Mandel
1970 Journal of Research of the National Bureau of Standards Section B Mathematical Sciences  
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

Leonardo Vianna do Nascimento, Ana L C Bazzan
2005 Genetics and Molecular Research  
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]

Agnieszka Danek, Rafał Pokrzywa, Izabela Makałowska, Andrzej Polański
2012 Lecture Notes in Computer Science  
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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