12,734 research outputs found
Laboratory Bounds on Electron Lorentz Violation
Violations of Lorentz boost symmetry in the electron and photon sectors can
be constrained by studying several different high-energy phenomenon. Although
they may not lead to the strongest bounds numerically, measurements made in
terrestrial laboratories produce the most reliable results. Laboratory bounds
can be based on observations of synchrotron radiation, as well as the observed
absences of vacuum Cerenkov radiation. Using measurements of synchrotron energy
losses at LEP and the survival of TeV photons, we place new bounds on the three
electron Lorentz violation coefficients c_(TJ), at the 3 x 10^(-13) to 6 x
10^(-15) levels.Comment: 18 page
Back-translation for discovering distant protein homologies
Frameshift mutations in protein-coding DNA sequences produce a drastic change
in the resulting protein sequence, which prevents classic protein alignment
methods from revealing the proteins' common origin. Moreover, when a large
number of substitutions are additionally involved in the divergence, the
homology detection becomes difficult even at the DNA level. To cope with this
situation, we propose a novel method to infer distant homology relations of two
proteins, that accounts for frameshift and point mutations that may have
affected the coding sequences. We design a dynamic programming alignment
algorithm over memory-efficient graph representations of the complete set of
putative DNA sequences of each protein, with the goal of determining the two
putative DNA sequences which have the best scoring alignment under a powerful
scoring system designed to reflect the most probable evolutionary process. This
allows us to uncover evolutionary information that is not captured by
traditional alignment methods, which is confirmed by biologically significant
examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics
(WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009
Pairwise alignment incorporating dipeptide covariation
Motivation: Standard algorithms for pairwise protein sequence alignment make
the simplifying assumption that amino acid substitutions at neighboring sites
are uncorrelated. This assumption allows implementation of fast algorithms for
pairwise sequence alignment, but it ignores information that could conceivably
increase the power of remote homolog detection. We examine the validity of this
assumption by constructing extended substitution matrixes that encapsulate the
observed correlations between neighboring sites, by developing an efficient and
rigorous algorithm for pairwise protein sequence alignment that incorporates
these local substitution correlations, and by assessing the ability of this
algorithm to detect remote homologies. Results: Our analysis indicates that
local correlations between substitutions are not strong on the average.
Furthermore, incorporating local substitution correlations into pairwise
alignment did not lead to a statistically significant improvement in remote
homology detection. Therefore, the standard assumption that individual residues
within protein sequences evolve independently of neighboring positions appears
to be an efficient and appropriate approximation
NCBI BLAST: a better web interface
Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement
Bounding Isotropic Lorentz Violation Using Synchrotron Losses at LEP
Some deviations from special relativity--especially isotropic effects--are
most efficiently constrained using particles with velocities very close to 1.
While there are extremely tight bounds on some of the relevant parameters
coming from astrophysical observations, many of these rely on our having an
accurate understanding of the dynamics of high-energy sources. It is desirable
to have reliable laboratory constraints on these same parameters. The
fastest-moving particles in a laboratory were electrons and positrons at LEP.
The energetics of the LEP beams were extremely well understood, and
measurements of the synchrotron emission rate indicate that that any isotropic
deviation of the speed of light from 1 must be smaller than 5 x 10^(-15).Comment: 8 page
Simplified amino acid alphabets based on deviation of conditional probability from random background
The primitive data for deducing the Miyazawa-Jernigan contact energy or
BLOSUM score matrix consists of pair frequency counts. Each amino acid
corresponds to a conditional probability distribution. Based on the deviation
of such conditional probability from random background, a scheme for reduction
of amino acid alphabet is proposed. It is observed that evident discrepancy
exists between reduced alphabets obtained from raw data of the
Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous
sequence database SCOP40 as a test set, we detect homology with the obtained
coarse-grained substitution matrices. It is verified that the reduced alphabets
obtained well preserve information contained in the original 20-letter
alphabet.Comment: 9 pages,3figure
Clustering with shallow trees
We propose a new method for hierarchical clustering based on the optimisation
of a cost function over trees of limited depth, and we derive a
message--passing method that allows to solve it efficiently. The method and
algorithm can be interpreted as a natural interpolation between two well-known
approaches, namely single linkage and the recently presented Affinity
Propagation. We analyze with this general scheme three biological/medical
structured datasets (human population based on genetic information, proteins
based on sequences and verbal autopsies) and show that the interpolation
technique provides new insight.Comment: 11 pages, 7 figure
HMMER web server: interactive sequence similarity searching
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them
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