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SEGMENT: identifying compositional domains in DNA sequences
1999
Bioinformatics
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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
2001
Physical Review Letters
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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
2015
Evolutionary Bioinformatics
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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]
2007
arXiv
pre-print
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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
2004
PLoS Biology
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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
2009
PLoS ONE
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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
1996
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
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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
2010
Protein Science
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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
2002
Computers and Chemistry
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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
2009
Nucleic Acids Research
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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
2009
Molecular biology and evolution
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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
2008
Journal of Physics: Condensed Matter
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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
2010
Biochemistry
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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
2004
EURASIP Journal on Advances in Signal Processing
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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
2015
Proceedings of the National Academy of Sciences of the United States of America
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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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