File Name: an o nd difference algorithm and its variations .zip
Gauche is an R7RS Scheme implementation.
- Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
- Gauche (Scheme implementation)
- fast-diff – readme
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Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. Temperature, magnetic field, and linewidth measurements establish that these centers arise from excitons laterally localized at interface fluctuations. For sufficiently narrow wells, virtually all emission originates from such centers. Commentary: Harald Hess and I joined forces, combining my near-field optical technology with his cryogenic scanned probe microscope to produce the first paper on high resolution spectroscopy beyond the diffraction limit.
We discovered that the broad luminescence spectrum traditionally observed from quantum well heterostructures reflects a resolution-limited ensemble average of emission from numerous discrete sites of exciton recombination occurring at atomic-scale corrugations in the confining interfaces.
With the combination of high spatial resolution from near-field excitation and high spectral resolution from cryogenic operation, we were able to isolate these emission sites in a multidimensional space of xy position and wavelength, even though their density was too great to isolate them on the basis of spatial resolution alone.
This insight was very influential in the genesis of the concept see above that would eventually lead to far-field superresolution by PALM. New approaches in electrophysiology and molecular biology have provided a better understanding of the factors that determine the kinetics of excitatory postsynaptic currents. Recent studies suggest that the time course of neurotransmitter concentration in the synaptic cleft, the gating properties of the native channels, and the glutamate receptor subunit composition all appear to be important factors.
Aphid soldiers, altruistic larvae that protect the colony from predators, are an example of highly social behaviour in an insect group with a natural history different from the eusocial Hymenoptera and Isoptera.
Aphids therefore allow independent tests of theory developed to explain the evolution of eusociality. Although soldiers have been discovered in five tribes from two families, the number and pattern of origins and losses of soldiers is unknown due to a lack of phylogenetic data. Here I present a mtDNA based phylogeny for the Hormaphididae, and test the hypothesis that soldiers in the tribe Cerataphidini produced during two points in the life cycle represent independent origins.
The results support this hypothesis. In addition, a minimum of five evolutionary events, either four origins and one loss or five origins, are required to explain the distribution of soldiers in the family. The positions of the origins and losses are well resolved, and this phylogeny provides an historical framework for studies on the causes of soldier aphid evolution. These genes are required for cytokinesis, and their products are present at the bud neck during cell division. We find that pnut is also required for cytokinesis: in pnut mutants, imaginal tissues fail to proliferate and instead develop clusters of large, multinucleate cells.
Pnut protein is localized to the cleavage furrow of dividing cells during cytokinesis and to the intercellular bridge connecting postmitotic daughter cells.
In addition to its role in cytokinesis, pnut displays genetic interactions with seven in absentia, a gene required for neuronal fate determination in the compound eye, suggesting that pnut may have pleiotropic functions.
Our results suggest that this class of proteins is involved in aspects of cytokinesis that have been conserved between flies and yeast. The mass-weighted average structures in por-Si are particles, not wires, with dimensions significantly smaller than previously reported or proposed. The dendritic trees of neurons are structurally and functionally complex integrative units receiving thousands of synaptic inputs that have excitatory and inhibitory, fast and slow, and electrical and biochemical effects.
The pattern of activation of these synaptic inputs determines if the neuron will fire an action potential at any given point in time and how it will respond to similar inputs in the future.
Two critical factors affect the integrative function of dendrites: the distribution of voltage-gated ion channels in the dendritic tree and the passive electrical properties, or 'electrotonic structure', upon which these active channels are superimposed.
The authors review recent data from patch-clamp recordings that provide new estimates of the passive membrane properties of hippocampal neurons, and show, with examples, how these properties affect the shaping and attenuation of synaptic potentials as they propagate in the dendrites, as well as how they affect the measurement of current from synapses located in the dendrites.
Voltage-gated channels might influence the measurement of 'passive' membrane properties and, reciprocally, passive membrane properties might affect the activation of voltage-gated channels in dendrites. The function of the central nervous system as it controls sex-specific behaviors in Drosophila has been studied with renewed intensity, in the context of genetic factors that influence the development of sexually differentiated aspects of this insect.
Three categories of genetic variations that cause anomalies in courtship and mating behaviors are discussed: 1 mutants isolated with regard to courtship defects, of which putatively courtship-specific variants such as the fruitless mutant are a subset; 2 general behavioral and neurological variants including sensory and learning mutants , whose defects include subnormal reproductive performance; and 3 mutations of genes within the sex-determination regulatory hierarchy of Drosophila, the analysis of which has included studies of reproductive behavior.
Recent studies of mutations in two of these categories have provided new insights into the control of neuronally based aspects of sex-specific behavior. The doublesex gene, the final factor acting in the sex-determination hierarchy, had been previously thought to regulate all aspects of sexual differentiation.
Yet, it has been recently shown that doublesex does not control at least one neuronally-determined feature of sex-specific anatomy--a muscle in the male's abdomen, whose normal development is, however, dependent on the action of fruitless.
These considerations prompted us to examine further and in some cases re-examine the influences exerted by sex-determination hierarchy genes on behavior. Our results--notably those obtained from assessments of doublesex mutations' effects on general reproductive actions and on a particular component of the courtship sequence male "singing" behavior --lead to the suggestion that there is a previously unrecognized branch within the sex-determination hierarchy, which controls the differentiation of the male- and female- specific phenotypes of Drosophila.
This new branch separates from the doublesex-related one immediately before the action of that gene just after transformer and transformer-2 and appears to control as least some aspects of neuronally determined sexual differentiation of males.
Development of the Drosophila retina occurs asynchronously; differentiation, its front marked by the morphogenetic furrow, progresses across the eye disc epithelium over a 2 day period. We have investigated the mechanism by which this front advances, and our results suggest that developing retinal cells drive the progression of morphogenesis utilizing the products of the hedgehog hh and decapentaplegic dpp genes.
Analysis of hh and dpp genetic mosaics indicates that the products of these genes act as diffusible signals in this process. Expression of dpp in the morphogenetic furrow is closely correlated with the progression of the furrow under a variety of conditions. We show that hh, synthesized by differentiating cells, induces the expression of dpp, which appears to be a primary mediator of furrow movement.
Skip to main content. Items per page 5 10 20 40 Tjian Lab Rubin Lab. View PDF. View Publication Page. Spruston Lab. Curr Opin Neurobiol. Stern Lab. Proc Biol Sci. Rubin Lab. Harris Lab. Physical Review Letters. Trends Neurosci. Baker Lab. Baker B, Taylor B, Villella.
Gauche (Scheme implementation)
Motivation: Long arrays of near-identical tandem repeats are a common feature of centromeric and subtelomeric regions in complex genomes. These sequences present a source of repeat structure diversity that is commonly ignored by standard genomic tools. Unlike reads shorter than the underlying repeat structure that rely on indirect inference methods, e. By operating on reads prior to assembly, our approach provides a more comprehensive set of repeat-structure variants and is not impacted by rearrangements or sequence underrepresentation due to misassembly. The pipeline is designed to report local repeat organization summaries for each read, thereby monitoring rearrangements in repeat units, shifts in repeat orientation and sites of array transition into non-satellite DNA, typically defined by transposable element insertion.
The problems of finding a longest common subsequence of two sequences A and B and a shortest edit script for transforming A into B have long been known to be dual problems. Using this perspective, a simple O ND time and space algorithm is developed where N is the sum of the lengths of A and B and D is the size of the minimum edit script for A and B. The algorithm performs well when differences are small sequences are similar and is consequently fast in typical applications. This is a preview of subscription content, access via your institution. Rent this article via DeepDyve. Aho, D. Hirschberg, and J.
This article is about comparing text files and the proven, best and most famous algorythm to identify the differences between them. The source code that you can find in the download implements a small class with a simple to use API that just does this job. You should have it in the bag of your algorythms. Beside the class that implements the algorythm there is also a sample web application that compares 2 files and generates html output with a combined and colored document. In this article you can find a abstract recursive definition of the algorythm using some pseudo-code that needs to be transferred to a existing programming language. There are many C, Java, Lisp implementations public available of this algorythm out there on the internet.
fast-diff – readme
Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields. In this article, we present the wavefront alignment algorithm WFA , an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.
Myers[ 1 ]. Multiple variants of the algorithms discussed in Myers' paper are presented in this article, along with working source code versions of the pseudo-code presented in the paper. Two refinements to the linear-space Myers algorithm are also discussed. Finally, a proof-of-concept patch for GNU diffutils is included that produces slower execution for many typical use cases, but is asymptotically superior as the size difference between the files grows arbitrarily large when calculating the minimum edit difference. Some examples of how to make use of this function are provided later in this article.