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SEGMENT: identifying compositional domains in DNA sequences

J. L.Oliver, R. Roman-Roldan, J. Perez, P. Bernaola-Galvan
1999 Bioinformatics  
In a few simple sequences, domains can simply be identified by eye; however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current  ...  Motivation: DNA sequences are formed by patches or domains of different nucleotide composition.  ...  spatial compositional structure in DNA sequences.  ... 
doi:10.1093/bioinformatics/15.12.974 pmid:10745986 fatcat:revqblp6rndb3jimwmsejtjklq

New Stopping Criteria for Segmenting DNA Sequences

Wentian Li
2001 Physical Review Letters  
We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns.  ...  The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.  ...  Computational methods used to identify homogeneous regions are called segmentation procedures [2, 7] which are important for many DNA sequence analysis tasks: detecting the existence of isochores, identifying  ... 
doi:10.1103/physrevlett.86.5815 pmid:11415365 fatcat:gjzbtgxfnjen5bswykrtuoauxm

Segmenting the Human Genome into Isochores

Paolo Cozzi, Luciano Milanesi, Giorgio Bernardi
2015 Evolutionary Bioinformatics  
The human genome is a mosaic of isochores, which are long (>200 kb) DNA sequences that are fairly homogeneous in base composition and can be assigned to five families comprising 33%-59% of GC composition  ...  We present a critical discussion of the currently available methods and a new approach called isoSegmenter which allows segmenting the genome into isochores in a fast and completely automatic manner.  ...  In view of the results of Figure 4 , isoPlotter can only be defined as an exercise in DNA sequence segmentation with no biological relevance (which, in fact, was not claimed), as indicated by the lack  ... 
doi:10.4137/ebo.s27693 pmid:26640363 pmcid:PMC4662427 fatcat:z55l477z4jdgdmo6lozqlfvqka

Segmentation and Context of Literary and Musical Sequences [article]

Damian H. Zanette
2007 arXiv   pre-print
For the sonata, the segments correspond to tonal domains and reveal in detail the characteristic tonal progression of such kind of musical composition.  ...  The algorithm divides the sequences into segments of maximal compositional divergence between them.  ...  Acknowledgments I would like to thank Ana Majtey, from Universidad Nacional de Córdoba, Argentina, for pointing out the Jensen-Shannon divergence as a tool for the analysis of symbolic sequences.  ... 
arXiv:0707.0895v1 fatcat:4scmh2lgebaebetvp2b6yivfdi

Segmentally Variable Genes:A New Perspective on Adaptation

Yu Zheng, Richard J Roberts, Simon Kasif, Ford Doolittle
2004 PLoS Biology  
The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies.  ...  Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates.  ...  We thank all the sequencing teams who have made genome sequence data publicly available for analysis.  ... 
doi:10.1371/journal.pbio.0020081 pmid:15094797 pmcid:PMC387263 fatcat:bzibosm2q5hkfc7bplrvfwuwpq

Characterisation of Inactivation Domains and Evolutionary Strata in Human X Chromosome through Markov Segmentation

Ashwin Kelkar, Vivek Thakur, Ramakrishna Ramaswamy, Deepti Deobagkar, Sridhar Hannenhalli
2009 PLoS ONE  
Markov segmentation is a method of identifying compositionally different subsequences in a given symbolic sequence.  ...  We have applied this technique to the DNA sequence of the human X chromosome to analyze its compositional structure.  ...  In order to identify compositional elements that are potentially involved in effecting inactivation (or escape), the program TEIRESIAS [14] was used to identify patterns in the DNA sequences that are  ... 
doi:10.1371/journal.pone.0007885 pmid:19946363 pmcid:PMC2776969 fatcat:sfbusegfljfilhomcdjalwmrfm

Compositional segmentation and long-range fractal correlations in DNA sequences

Pedro Bernaola-Galván, Ramón Román-Roldán, José L. Oliver
1996 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
Some of the identified DNA domains were uncorrelated, but most of them continued to display long-range correlations even after several steps of recursive segmentation, thus indicating a complex multi-length-scaled  ...  On the other hand, by separately shuffling each segment, or by randomly rearranging the order in which the different segments occur in the sequence, shuffled sequences preserving the original statistical  ...  Segmentation procedure Our aim is to divide a sequence into segments in such a way as to maximize the compositional divergence between the resulting DNA domains.  ... 
doi:10.1103/physreve.53.5181 pmid:9964850 fatcat:adekqmbbpbheniuzk3hdltmao4

CTCF terminal segments are unstructured

Selena R. Martinez, JJ L. Miranda
2010 Protein Science  
This protein consists of 11 zinc fingers flanked by polypeptide segments of unknown structure and function.  ...  The human CCCTC-binding factor, CTCF, organizes and regulates transcription of the genome by colocalizing distant DNA elements on the same and even different chromosomes.  ...  for poly(ADP-ribosyl)ation in vitro. 37 Moreover, the classical zinc fingers of CTCF bind DNA, 1,38 but these domains in other transcription factors also bind proteins. 39, 40 We now know that CTCF  ... 
doi:10.1002/pro.367 pmid:20196073 pmcid:PMC2868253 fatcat:7fwmvlaa3bhwjmyzhjlmerxxhe

Applications of recursive segmentation to the analysis of DNA sequences

Wentian Li, Pedro Bernaola-Galván, Fatameh Haghighi, Ivo Grosse
2002 Computers and Chemistry  
Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T.  ...  We apply various conversion schemes in order to address the following five DNA sequence analysis problems: isochore mapping, CpG island detection, locating the origin and terminus of replication in bacterial  ...  K01HG00024, PBG is partially supported by the grant BI099-0651-CO2-01 from the Spanish Government, FH's work is supported by grants from PhRMA foundation, NSF (DBI-0078523), and Sloan/ DOE Fellowship in  ... 
doi:10.1016/s0097-8485(02)00010-4 pmid:12144178 fatcat:5akn3j2wcrcydf6kwl5ijofqs4

Detection of genomic islands via segmental genome heterogeneity

Aaron J. Arvey, Rajeev K. Azad, Alpan Raval, Jeffrey G. Lawrence
2009 Nucleic Acids Research  
This approach is based on a generalized divergence measure to quantify the compositional difference between segments in a hypothesis-testing framework.  ...  The weakness of these 'bottom-up' approaches lies in the difficulty in identifying robustly those genes which are atypical, or phylogenetically restricted, due to recent foreign ancestry.  ...  Therefore, we conclude that the MJSD metric is robust in identifying segment boundaries within DNA sequences without regard to gene boundaries.  ... 
doi:10.1093/nar/gkp576 pmid:19589805 pmcid:PMC2760805 fatcat:afsdjcdjdnhfxlto3hkrocqsse

Comparative Testing of DNA Segmentation Algorithms Using Benchmark Simulations

Eran Elhaik, Dan Graur, Krešimir Josić
2009 Molecular biology and evolution  
Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability.  ...  The sequences in the second set are composed of a mosaic of many short domains and a few long ones, distinguished by sharp GC content boundaries between neighboring domains.  ...  We thank Laurent Guéguen for his help in using the Sarment algorithm.  ... 
doi:10.1093/molbev/msp307 pmid:20018981 fatcat:fuxweir3ezc3zl7rnyqym7vfou

Segmentation of DNA sequences into twostate regions and melting fork regions

Eivind Tøstesen, Geir Kjetil Sandve, Fang Liu, Eivind Hovig
2008 Journal of Physics: Condensed Matter  
In this paper, we introduce a new approach to identify the twostate regions and melting fork regions along a given DNA sequence.  ...  Compared with an ad hoc segmentation used in one of our previous studies, the new algorithm is based on boundary probability profiles, rather than standard melting maps.  ...  The stability and melting temperature of a domain not only depends on its internal sequence composition, but also on the stabilities of adjacent domains.  ... 
doi:10.1088/0953-8984/21/3/034109 pmid:21817254 fatcat:wtl4ddqynzefzpows2cwvh7iqu

Identification of a Regulatory Segment of Poly(ADP-ribose) Glycohydrolase

Davide Botta, Myron K. Jacobson
2010 Biochemistry  
Expression and analysis of human PARG segments identified a minimal catalytically active C-terminal PARG (hPARG59) containing a 16residue N-terminal mitochondrial targeting sequence (MTS).  ...  histones, p53 and enzymes involved in DNA repair (6).  ...  Acknowledgments DNA sequence analyses were performed by the University of Arizona Genetic Analysis and Technology Core Service Facility.  ... 
doi:10.1021/bi100973m pmid:20684510 pmcid:PMC2939713 fatcat:t37ahb445zgspo5oyq5wumnyaq

Segmentation of DNA into Coding and Noncoding Regions Based on Recursive Entropic Segmentation and Stop-Codon Statistics

Daniel Nicorici, Jaakko Astola
2004 EURASIP Journal on Advances in Signal Processing  
coding and noncoding regions in DNA sequences.  ...  Recursively, we apply a new entropic segmentation method on DNA sequences using Jensen-Shannon and Jensen-Rényi divergences in order to find the borders between coding and noncoding DNA regions.  ...  They are important for DNA-sequence analysis when identifying the borders between coding and noncoding regions [5, 7, 19, 20] .  ... 
doi:10.1155/s1110865704309212 fatcat:utn4ileicfd2vk4lx5wxxph73a

Generating new prions by targeted mutation or segment duplication

Kacy R. Paul, Connor G. Hendrich, Aubrey Waechter, Madison R. Harman, Eric D. Ross
2015 Proceedings of the National Academy of Sciences of the United States of America  
This (A) Short segments lacking any prion-inhibiting amino acids were identified in the Puf4 PrLD (indicated as α, β, γ, and δ in the PrLD sequence).  ...  (14) identified 100 yeast fragments with prion-like composition and tested each in four assays for prion-like activity.  ... 
doi:10.1073/pnas.1501072112 pmid:26100899 pmcid:PMC4507246 fatcat:vtf7vm2l2zcdrj4kdowrcmaoea
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