167 research outputs found
Scaling Laws and Similarity Detection in Sequence Alignment with Gaps
We study the problem of similarity detection by sequence alignment with gaps,
using a recently established theoretical framework based on the morphology of
alignment paths. Alignments of sequences without mutual correlations are found
to have scale-invariant statistics. This is the basis for a scaling theory of
alignments of correlated sequences. Using a simple Markov model of evolution,
we generate sequences with well-defined mutual correlations and quantify the
fidelity of an alignment in an unambiguous way. The scaling theory predicts the
dependence of the fidelity on the alignment parameters and on the statistical
evolution parameters characterizing the sequence correlations. Specific
criteria for the optimal choice of alignment parameters emerge from this
theory. The results are verified by extensive numerical simulations.Comment: 25 pages, 11 figure
Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation
Differences in the regional substitution patterns in the human genome created
patterns of large-scale variation of base composition known as genomic
isochores. To gain insight into the origin of the genomic isochores we develop
a maximum likelihood approach to determine the history of substitution patterns
in the human genome. This approach utilizes the vast amount of repetitive
sequence deposited in the human genome over the past ~250 MYR. Using this
approach we estimate the frequencies of seven types of substitutions: the four
transversions, two transitions, and the methyl-assisted transition of cytosine
in CpG. Comparing substitutional patterns in repetitive elements of various
ages, we reconstruct the history of the base-substitutional process in the
different isochores for the past 250 Myr. At around 90 Myr ago (around the time
of the mammalian radiation), we find an abrupt 4- to 8-fold increase of the
cytosine transition rate in CpG pairs compared to that of the reptilian
ancestor. Further analysis of nucleotide substitutions in regions with
different GC-content reveals concurrent changes in the substitutional patterns.
While the substitutional pattern was dependent on the regional GC-content in
such ways that it preserved the regional GC-content before the mammalian
radiation, it lost this dependence afterwards. The substitutional pattern
changed from an isochore-preserving to an isochore-degrading one. We conclude
that isochores have been established before the radiation of the eutherian
mammals and have been subject to the process of homogenization since then
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects
This study presents the first global, 1 Mbp level analysis of patterns of
nucleotide substitutions along the human lineage. The study is based on the
analysis of a large amount of repetitive elements deposited into the human
genome since the mammalian radiation, yielding a number of results that would
have been difficult to obtain using the more conventional comparative method of
analysis. This analysis revealed substantial and consistent variability of
rates of substitution, with the variability ranging up to 2-fold among
different regions. The rates of substitutions of C or G nucleotides with A or T
nucleotides vary much more sharply than the reverse rates suggesting that much
of that variation is due to differences in mutation rates rather than in the
probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all
types of substitution we observe substantially more hotspots than coldspots,
with hotspots showing substantial clustering over tens of Mbp's. Our analysis
revealed that GC-content of surrounding sequences is the best predictor of the
rates of substitution. The pattern of substitution appears very different near
telomeres compared to the rest of the genome and cannot be explained by the
genome-wide correlations of the substitution rates with GC content or exon
density. The telomere pattern of substitution is consistent with natural
selection or biased gene conversion acting to increase the GC-content of the
sequences that are within 10-15 Mbp away from the telomere.Comment: 35 pages, 6 figure
Deterministic characterization of stochastic genetic circuits
For cellular biochemical reaction systems where the numbers of molecules is
small, significant noise is associated with chemical reaction events. This
molecular noise can give rise to behavior that is very different from the
predictions of deterministic rate equation models. Unfortunately, there are few
analytic methods for examining the qualitative behavior of stochastic systems.
Here we describe such a method that extends deterministic analysis to include
leading-order corrections due to the molecular noise. The method allows the
steady-state behavior of the stochastic model to be easily computed,
facilitates the mapping of stability phase diagrams that include stochastic
effects and reveals how model parameters affect noise susceptibility, in a
manner not accessible to numerical simulation. By way of illustration we
consider two genetic circuits: a bistable positive-feedback loop and a
negative-feedback oscillator. We find in the positive feedback circuit that
translational activation leads to a far more stable system than transcriptional
control. Conversely, in a negative-feedback loop triggered by a
positive-feedback switch, the stochasticity of transcriptional control is
harnessed to generate reproducible oscillations.Comment: 6 pages (Supplementary Information is appended
Polymer Adsorption on Disordered Substrate
We analyze the recently proposed "pattern-matching" phase of a Gaussian
random heteropolymer adsorbed on a disordered substrate [S. Srebnik, A.K.
Chakraborty and E.I. Shakhnovich, Phys. Rev. Lett. 77, 3157 (1996)]. By mapping
the problem to that of a directed homopolymer in higher-dimensional random
media, we show that the pattern-matching phase is asymptotically weakly
unstable, and the large scale properties of the system are given by that of an
adsorbed homopolymer.Comment: 5 pages, RevTeX, text also available at http://matisse.ucsd.edu/~hw
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