101 research outputs found
A standalone version of IsoFinder for the computational prediction of isochores in genome sequences
Isochores are long genome segments relatively homogeneous in G+C. A heuristic
algorithm based on entropic segmentation has been developed by our group, and a
web server implementing all the required components is available. However, a
researcher may want to perform batch processing of many sequences
simultaneously in its local machine, instead of analyzing them on one by one
basis through the web. To this end, standalone versions are required. We report
here the implementation of two standalone programs, able to predict isochores
at the sequence level: 1) a command-line version (IsoFinder) for Windows and
Linux systems; and 2) a user-friendly version (IsoFinderWin) running under
Windows.Comment: 7 pages, 3 figure
Isochores Merit the Prefix 'Iso'
The isochore concept in human genome sequence was challenged in an analysis
by the International Human Genome Sequencing Consortium (IHGSC). We argue here
that a statement in IGHSC analysis concerning the existence of isochore is
incorrect, because it had applied an inappropriate statistical test. To test
the existence of isochores should be equivalent to a test of homogeneity of
windowed GC%. The statistical test applied in the IHGSC's analysis, the
binomial test, is however a test of a sequence being random on the base level.
For testing the existence of isochore, or homogeneity in GC%, we propose to use
another statistical test: the analysis of variance (ANOVA). It can be shown
that DNA sequences that are rejected by binomial test may not be rejected by
the ANOVA test.Comment: 14 pages (including 1 figure), submitte
Simplifying the mosaic description of DNA sequences
By using the Jensen-Shannon divergence, genomic DNA can be divided into
compositionally distinct domains through a standard recursive segmentation
procedure. Each domain, while significantly different from its neighbours, may
however share compositional similarity with one or more distant
(non--neighbouring) domains. We thus obtain a coarse--grained description of
the given DNA string in terms of a smaller set of distinct domain labels. This
yields a minimal domain description of a given DNA sequence, significantly
reducing its organizational complexity. This procedure gives a new means of
evaluating genomic complexity as one examines organisms ranging from bacteria
to human. The mosaic organization of DNA sequences could have originated from
the insertion of fragments of one genome (the parasite) inside another (the
host), and we present numerical experiments that are suggestive of this
scenario.Comment: 16 pages, 1 figure, Accepted for publication in Phys. Rev.
Phylogenetic distribution of large-scale genome patchiness
[Background]
The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level.
[Results]
The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range.
[Conclusion]
Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.This work was supported by the Spanish Government (BIO2005-09116-C03-01) and Plan Andaluz de InvestigaciĂłn (CVI-162, P06-FQM-01858, P07-FQM-03163 and TIC-640)
Finite-sample frequency distributions originating from an equiprobability distribution
Given an equidistribution for probabilities p(i)=1/N, i=1..N. What is the
expected corresponding rank ordered frequency distribution f(i), i=1..N, if an
ensemble of M events is drawn?Comment: 4 pages, 4 figure
Scaling analysis of multivariate intermittent time series
The scaling properties of the time series of asset prices and trading volumes
of stock markets are analysed. It is shown that similarly to the asset prices,
the trading volume data obey multi-scaling length-distribution of
low-variability periods. In the case of asset prices, such scaling behaviour
can be used for risk forecasts: the probability of observing next day a large
price movement is (super-universally) inversely proportional to the length of
the ongoing low-variability period. Finally, a method is devised for a
multi-factor scaling analysis. We apply the simplest, two-factor model to
equity index and trading volume time series.Comment: 16 pages, 5 figures, accepted for publication in Physica
New stopping criteria for segmenting DNA sequences
We propose a solution on the stopping criterion in segmenting inhomogeneous
DNA sequences with complex statistical patterns. This new stopping criterion is
based on Bayesian Information Criterion (BIC) in the model selection framework.
When this stopping criterion is applied to a left telomere sequence of yeast
Saccharomyces cerevisiae and the complete genome sequence of bacterium
Escherichia coli, borders of biologically meaningful units were identified
(e.g. subtelomeric units, replication origin, and replication terminus), and a
more reasonable number of domains was obtained. We also introduce a measure
called segmentation strength which can be used to control the delineation of
large domains. The relationship between the average domain size and the
threshold of segmentation strength is determined for several genome sequences.Comment: 4 pages, 4 figures, Physical Review Letters, to appea
Phase Transition in a Random Fragmentation Problem with Applications to Computer Science
We study a fragmentation problem where an initial object of size x is broken
into m random pieces provided x>x_0 where x_0 is an atomic cut-off.
Subsequently the fragmentation process continues for each of those daughter
pieces whose sizes are bigger than x_0. The process stops when all the
fragments have sizes smaller than x_0. We show that the fluctuation of the
total number of splitting events, characterized by the variance, generically
undergoes a nontrivial phase transition as one tunes the branching number m
through a critical value m=m_c. For m<m_c, the fluctuations are Gaussian where
as for m>m_c they are anomalously large and non-Gaussian. We apply this general
result to analyze two different search algorithms in computer science.Comment: 5 pages RevTeX, 3 figures (.eps
Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals
We investigate how various coarse-graining methods affect the scaling
properties of long-range power-law correlated and anti-correlated signals,
quantified by the detrended fluctuation analysis. Specifically, for
coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii)
the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find,
that for anti-correlated signals coarse-graining in the magnitude leads to a
crossover to random behavior at large scales, and that with increasing the
width of the coarse-graining partition interval this crossover moves
to intermediate and small scales. In contrast, the scaling of positively
correlated signals is less affected by the coarse-graining, with no observable
changes when a crossover appears at small
scales and moves to intermediate and large scales with increasing . For
very rough coarse-graining () based on the Floor and Symmetry
methods, the position of the crossover stabilizes, in contrast to the
Centro-Symmetry method where the crossover continuously moves across scales and
leads to a random behavior at all scales, thus indicating a much stronger
effect of the Centro-Symmetry compared to the Floor and the Symmetry methods.
For coarse-graining in time, where data points are averaged in non-overlapping
time windows, we find that the scaling for both anti-correlated and positively
correlated signals is practically preserved. The results of our simulations are
useful for the correct interpretation of the correlation and scaling properties
of symbolic sequences.Comment: 19 pages, 13 figure
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