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Speeding up the detection of evolutive tandem repeats

Richard Groult, Martine Léonard, Laurent Mouchard
2004 Theoretical Computer Science  
We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. consist in a series of almost contiguous copies having the following property: the Hamming distance between two  ...  It is based on the progressive computation of distances between candidate copies participating to the evolutive tandem repeat.  ...  tandem repeats with jumps using the Hamming distance.  ... 
doi:10.1016/s0304-3975(03)00423-7 fatcat:wihjzka4hbewtjommt2xirmtl4

Tandem repeats over the edit distance

D. Sokol, G. Benson, J. Tojeira
2007 Bioinformatics  
We present a precise definition for tandem repeats over the edit distance and an efficient, deterministic algorithm for finding these repeats.  ...  Although tandem repeats have been used by biologists for many years, there are few tools available for performing an exhaustive search for all tandem repeats in a given sequence.  ...  In (Groult et al., 2004; Hammock and Young, 2005) , evolutive tandem repeats are defined over the Hamming distance as follows.  ... 
doi:10.1093/bioinformatics/btl309 pmid:17237101 fatcat:suwnfk2m75hulbmf4a5g3yw43q

DNA repeats detection using a dedicated dot-plot analysis

Petre G. Pop
2015 2015 38th International Conference on Telecommunications and Signal Processing (TSP)  
DNA repeats are believed to play significant roles in genome evolution and diseases.  ...  The final images that best put in evidence the presence of repeated sequences were obtained using weighted cosine cross-correlation, Jukes-Cantor distance and Motyka similarity.  ...  In our experiments we used Hamming distance and Jukes-Cantor distance (an evolutionary distance).  ... 
doi:10.1109/tsp.2015.7296434 dblp:conf/tsp/Pop15 fatcat:j3ecfamzsnga3h4hrnlvjjjmte

DNA Repeats Detection Using a Dedicated Dot-Plot Analysis

Gavril Petre Pop
2015 International Journal of Advances in Telecommunications, Electrotechnics, Signals and Systems  
DNA repeats are believed to play significant roles in genome evolution and diseases.  ...  The final images that best put in evidence the presence of repeated sequences were obtained using weighted cosine cross-correlation, Jukes-Cantor distance and Motyka similarity.  ...  In our experiments we used Hamming distance and Jukes-Cantor distance (an evolutionary distance).  ... 
doi:10.11601/ijates.v4i3.140 fatcat:bkuqghhwgrd6nie7zogxfabrr4

A visual tool for DNA repeats screening

Petre G. Pop, Mircea F. Vaida
2015 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)  
The detection of tandem repeats is important in biology and medicine as it can be used for phylogenic studies and disease diagnosis.  ...  A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length.  ...  Tandem repeats can also be used for disease diagnosis.  ... 
doi:10.1109/embc.2015.7320296 pmid:26738196 dblp:conf/embc/PopV15 fatcat:qlz7antixvbq7gaibzd2ltdkz4

Data-Driven Insights into Deletions of Mycobacterium tuberculosis Complex Chromosomal DR Region Using Spoligoforests

Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Bulent Yener, Kristin P. Bennett
2011 2011 IEEE International Conference on Bioinformatics and Biomedicine  
Based on the contiguous deletion assumption and rare observation of convergent evolution, we first generate the most parsimonious forest of spoligotypes, called a spoligoforest, using three genetic distance  ...  In this study, we present an evolution model of spoligotype rearrangements using MIRU patterns to disambiguate the ancestors of spoligotypes, in a large patient dataset from the United States Centers for  ...  Similarly, the Hamming distance between MIRU patterns is defined as the number of MIRU loci with different number of tandem repeats: where m⃗ jr represents the number of repeats at MIRU locus r of 12-loci  ... 
doi:10.1109/bibm.2011.64 pmid:22343484 pmcid:PMC3279189 fatcat:xe3syt2krnewxnz65c4qkfbple

Finding Approximate Tandem Repeats With The Burrows-Wheeler Transform

Agnieszka Danek, Rafał Pokrzywa
2012 Zenodo  
This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance.  ...  They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases.  ...  If the Hamming distance is different than k, candidate from the current position is rejected. 3) Extending found double tandem repeats In the last stage, the double k-mismatch tandem repeat found is  ... 
doi:10.5281/zenodo.1055359 fatcat:3r7ma7zkffeelklncgbp25gsu4

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
2007 PLoS Computational Biology  
Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution  ...  Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.  ...  As input, we used the set of alpha-satellite repeat units S¼fs 1 , s 2 , . . ., s n g and a distance function d (s i , s j ) that returns aligned Hamming distance of two sequences s i , s j .  ... 
doi:10.1371/journal.pcbi.0030181 pmid:17907796 pmcid:PMC1994983 fatcat:w226zyquyva3zfcae5bpbxlo34

Inferred Spoligoforest Topology Unravels Spatially Bimodal Distribution of Mutations in the DR Region

C. Ozcaglar, A. Shabbeer, N. Kurepina, N. Rastogi, B. Yener, K. P. Bennett
2012 IEEE Transactions on Nanobioscience  
Based on the contiguous deletion assumption and rare observation of convergent evolution, we first generate the most parsimonious forest of spoligotypes, called a spoligoforest, using three genetic distance  ...  In this study, we present an evolution model of spoligotype rearrangements using MIRU patterns to disambiguate the ancestors of spoligotypes.  ...  Similarly, the Hamming distance between MIRU patterns is defined as the number of MIRU loci with different number of tandem repeats where represents the number of repeats at MIRU locus of 12-loci MIRU  ... 
doi:10.1109/tnb.2012.2213265 pmid:22987125 fatcat:heoukuvv3vfcjidwccdmjmsu4e

A SURVEY ON ALGORITHMIC ASPECTS OF TANDEM REPEATS EVOLUTION

ERIC RIVALS
2004 International Journal of Foundations of Computer Science  
Rivals A Survey on Algorithmic Aspects of Tandem Repeats Evolution 227 mutations. When one wishes to establish the common ancestry of any two genes, one first searches for sequence similarity.  ...  Local repetitions in genomes are called tandem repeats. A tandem repeat contains multiple, but slightly different copies of a repeated unit.  ...  In the first and second cases respectively, the authors use the Hamming and the Levenshtein distances on Σ * .  ... 
doi:10.1142/s012905410400239x fatcat:z7zlwpdt6ze6dfsjn5kl2jo7bi

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  
Tandem repeats (TRs) are contiguous copies of repeating patterns, which may be either exact or approximate.  ...  Approximate tandem repeats (ATRs) in a genomic sequences are adjacent copies of a repeating pattern of nucleotides, where similarity is defined by a suitable measure.  ...  Therefore, a group of repeats of length d will be used to find candidates for K-mismatch double ATR only for periods p satisfying the equation (2) The Hamming distance is calculated between consecutive  ... 
doi:10.1007/978-3-642-34123-6_23 fatcat:2fsr34gpija5dhrsf6hb7o3u6q

Understanding and identifying amino acid repeats

H. Luo, H. Nijveen
2013 Briefings in Bioinformatics  
Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution.  ...  repeats.  ...  He conceived and supervised the Protein Repeat project, which was supported partly by the BioRange project of the Netherlands Bioinformatics Centre (NBIC).  ... 
doi:10.1093/bib/bbt003 pmid:23418055 pmcid:PMC4103538 fatcat:lnsltvfxszbmvm7kygw6niefmm

TRStalker: an efficient heuristic for finding fuzzy tandem repeats

Marco Pellegrini, M. Elena Renda, Alessio Vecchio
2010 Computer applications in the biosciences : CABIOS  
Availability: TRStalker will be integrated in the Web-based Tandem Repeats Discovery Service (TReaDS) at  ...  Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity.  ...  In (Krishnan and Tang, 2004) it is used a definition similar to that of the Neighboring Approximate Tandem Repeat, except that the Hamming distance is used and that the threshold is not absolute but  ... 
doi:10.1093/bioinformatics/btq209 pmid:20529928 pmcid:PMC2881393 fatcat:ssv3p7l755fqbfyh77fv677vj4

Natural Selection Promotes Antigenic Evolvability

Christopher J. Graves, Vera I. D. Ros, Brian Stevenson, Paul D. Sniegowski, Dustin Brisson, Richard Moxon
2013 PLoS Pathogens  
This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation.  ...  Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE.  ...  Tandem-repeat motifs were identified using the mreps server [57] and majority-rule consensus sequences of the repeats were reported (75% threshold).  ... 
doi:10.1371/journal.ppat.1003766 pmid:24244173 pmcid:PMC3828179 fatcat:nihffm7be5fzdff5vkrl47tyhe

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections

Leonid Chindelevitch, Caroline Colijn, Prashini Moodley, Douglas Wilson, Ted Cohen, Mark M. Tanaka
2016 PLoS Computational Biology  
Once the complex infections are resolved into their constituent strains, ClassTR probabilistically classifies isolates as clonally heterogeneous or mixed by using a model of tandem repeat evolution.  ...  ClassTR uses optimization to resolve complex strains into simple strains and explicit models of tandem repeat evolution to classify the infections as clonal (due to within-host diversification) or mixed  ...  Sarah Otto for a useful suggestion, Dr. Pia Abel zur Wiesch for helpful discussions and Wendolyn Hill for help in preparing the figures. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004475 pmid:26829497 pmcid:PMC4734664 fatcat:4srvqw4c7zbs5givpm4xqcmxce
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