Figure - available via license: Creative Commons Attribution 2.0 Generic
Content may be subject to copyright.
The AAATTT-spectrum set analysis taken across all sequence data in a pool. The Burkholderia pseudomallei sequence data, having elevated proportions of the motifs of this spectrum set, create a contrast from those of Clostridium tetani and Staphylococcus aureus. These organisms are observed to have mixed proportions by this heatmap.
Source publication
On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutation...
Similar publications
This article boards the information model included in recall process of a national
company assembler. The study was developed considering the data flow and
information associated to the stages that compose the management boarding of product lifecycle (Product Lifecycle Management – PLM). The results demonstrate
the correct administration importance...
Bien que les applications utilisant les modèles 3D soient de plus en plus nombreuses, la création des modèles 3D en elle-même reste une tâche fastidieuse. La modélisation à partir d’exemples rend cette étape plus efficace en permettant à l'utilisateur d’exploiter des modèles existants pour les assembler afin d’obtenir un nouveau modèle. Les méthode...
This paper describes the implementation of a garbage collector as an undergraduate research project. The garbage collector is a continuation of a project where an Assembler, Virtual Machine and Compiler were implemented as a capstone project. The project required modifying the compiler to allocate memory compatible with a mark and sweep algorithm,...
Primordial germ cells are the progenitor cells that give rise to the gametes. In some animals, the germline is induced by zygotic transcription factors, whereas in others, primordial germ cell specification occurs via inheritance of maternally provided gene products known as germ plasm. Once specified, the primordial germ cells of some animals must...
As software permeates more and more aspects of daily life and becomes a central component of critical systems around the world,
software quality and effective methods to ensure it are paramount.
There is a huge variety of both static and dynamic analyses that aim to provide such guarantees.
Typically, such analyses are based on the analysed program...
Citations
... Because of the common hardships of applying limited computing resources to processing voluminous quantities of data, a statistical analysis is often appropriate [24,25]. Furthermore, frequency analysis is especially well suited for comparing large data sets and discovery, as it embraces convenient techniques of network analysis to ascertain natural patterns [26,27]. ...
Post-translational modifications (PTMs) are important steps in the biosynthesis of proteins. Aside from their integral contributions to protein development, i.e. perform specialized proteolytic cleavage of regulatory subunits, the covalent addition of functional groups of proteins or the degradation of entire proteins, PTMs are also involved in enabling proteins to withstand and recover from temporary environmental stresses (heat shock, microgravity and many others). The literature supports evidence of thousands of recently discovered PTMs, many of which may likely contribute similarly (perhaps, even, interchangeably) to protein stress response. Although there are many PTM actors on the biological stage, our study determines that these PTMs are generally cast into organism-specific, preferential roles. In this work, we study the PTM compositions across the mitochondrial (Mt) and non-Mt proteomes of 11 diverse organisms to illustrate that each organism appears to have a unique list of PTMs, and an equally unique list of PTM-associated residue reaction sites (RSs), where PTMs interact with protein. Despite the present limitation of available PTM data across different species, we apply existing and current protein data to illustrate particular organismal biases. We explore the relative frequencies of observed PTMs, the RSs and general amino-acid compositions of Mt and non-Mt proteomes. We apply these data to create networks and heatmaps to illustrate the evidence of bias. We show that the number of PTMs and RSs appears to grow along with organismal complexity, which may imply that environmental stress could play a role in this bias.
... However, due to the production of too small contigs, these systems are not able to completely assemble the whole genome of an organism (Ramos et al. 2013). In other words, since in these approaches the reads are assembled based on sufficient overlaps between short fragments there is a higher chance for mis-assemblies of the fragments (Bonham-Carter et al. 2013). Therefore, a hybrid approach such as Graphic Contig Analyzer for All Sequencing Platforms G4ALL (Ramos et al. 2013), MaSuRCA (Zimin et al. 2013) and PRICE (paired-read iterative contig extension) (Ruby et al. 2013) increase the sensitivity and accuracy of gene assembly. ...
Since most microorganisms in natural environments cannot be cultured in laboratory media, due to low growth rates or their dependency on specific conditions, culture-based systems are unable to estimate the full microbial diversity of an environment. However, molecular techniques can provide this ability by analysing the diversity of macromolecules, such as proteins, RNA or DNA, present in the environment. Metagenomic methods employ sequencing procedures for the determination of the microbial diversity of a community (sequence-driven metagenomic analysis) or for examining a particular functional ability of microorganisms in the environment (function-driven metage-nomic gene identification), using genomic DNA obtained directly from environmental samples. Application of metagenomic methods provides a huge amount of data that can be analysed only by using powerful computational bioinformatics tools. Currently, these bioinformatic tools are adequate to allow the ecological structure of a community and the possible functions of its members to be determined. The resulting data can be useful for phylogenetic and biotechnological studies. This paper reviews the emergence of new technologies based on sequencing environmental DNA and on bioinformatics. We assess its potential for application in environmental studies, particularly for developing new biomolecules that can be applied to degrading recalcitrant pollutants in terrestrial and aquatic systems.
... According to this classification, our method belongs to the composition vector based on k-word position. Based on Bonham-Carter et al. (2013), the basic steps of creating composition vectors based on k-word position are the following: (i) find the positions of the motifs in a sequence, (ii) create a vector by organizing the positions in some order, (iii) compute the distance between every two composition vectors to form a distance matrix, and optionally (iv) construct the phylogenic tree based on the differences. ...
... A frequency analysis is well suited for comparing large datasets [4,5]. To calculate the PTM frequencies, we parsed the Uniprot protein records concerning protein modification. ...
A post-translational modification (PTM) describes a form of biosynthesis for the task of initializing proteins for specific functions. PTMs are complexes which are involved in developing or customizing proteins to increase their functional diversity. In times of protein stress, PTMs may be involved in altering protein structures to allow for better chances of survival. Once the stress-condition has elapsed, PTMs are able to transform the protein's structure back to its original form for the continued survival of the protein. PTMs are not applied uniformly across organismal proteins and differing PTM preferences and usages may often exist between proteins of the same organism. Here, we study the frequency of factors (PTM predominance and their associated active sites, tRNAs and amino acids) which likely influence a PTM bias. We extract and study these factor frequencies across both mitochondrial (Mt) and non-Mt proteins of nine diverse organisms (closely following two, Arabidopsis thaliana and Caenorhabditis elegans, due to space limitations) to illustrate their remarkable differences which may strongly influence natural PTM selection. By this work, we offer evidence to argue that this PTM bias may be the result of these factors which combine in a poorly understood system to affect and control PTM interactions. Our analysis is made up of an application of frequency information concerning PTMs, active sites, tRNA and amino acids and is used to create network models for the clear visualization of its mechanisms for this PTM natural selection.
