Search results for " code"

Genes, genomes, and codes : revisiting some key terms with multiple meanings

2015

Is a genome the full complement of an organism?s genes or of its DNA? Is genetics the study of genes or of heredity? Is the genetic code the mechanism for translating nucleotide sequence to amino acid sequence or to phenotype? Does «genetic information» refer to the sequences coding for proteins or to all DNA sequences? Each of these questions stems from an elision between one, concrete, meaning, and another, open-ended and ambiguous. Such elision invites the illusion that the ambiguity of the open-ended term has been resolved, and by implication, that the gap between actual achievement and promise has been closed. Yet, despite the phenomenal progress molecular biology has made, we remain w…

2014

The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorp…

Methyl-CpG-binding proteins

2000

CpG methylation, the most common epigenetic modification of vertebrate genomes, is primarily associated with transcriptional repression. MeCP2, MBD1, MBD2, MBD3 and MBD4 constitute a family of vertebrate proteins that share the methyl-CpG-binding domain (MBD). The MBD, consisting of about 70 residues, possesses a unique alpha/beta-sandwich structure with characteristic loops, and is able to bind single methylated CpG pairs as a monomer. All MBDs except MBD4, an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1, form complexes with histone deacetylase. It has been established that MeCP2, MBD1 and MBD2 are involved in histone deacetylase-dependent repression and it i…

MetaCache-GPU: Ultra-Fast Metagenomic Classification

2021

The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is commonly facilitated by constructing index data structures which allow for efficient querying of substrings. Recent metagenomic classification pipelines annotate reads with taxonomic labels by analyzing their $k$-mer histograms with respect to a reference genome database. CPU-based index construction is often performed in a preprocessing phase due to the relatively high cost of building irregular data structures such as hash maps. However, the rapidly growi…

Histone Code and Higher-Order Chromatin Folding: A Hypothesis

2016

AbstractHistone modifications alone or in combination are thought to modulate chromatin structure and function; a concept termed histone code. By combining evidence from several studies, we investigated if the histone code can play a role in higher-order folding of chromatin. Firstly using genomic data, we analyzed associations between histone modifications at the nucleosome level. We could dissect the composition of individual nucleosomes into five predicted clusters of histone modifications. Secondly, by assembling the raw reads of histone modifications at various length scales, we noticed that the histone mark relationships that exist at nucleosome level tend to be maintained at the high…

Blockchain Tokens From the Perspective of German Civil Law: An Updated View

2020

Tokens are increasingly being generated on the basis of blockchain technology, which are intended to embody certain rights and obligations as cryptographically secured electronic coupons or digital coupons or vouchers . This paper provides an overview of the current state of affairs and the legal discussion of recent years and examines the extent to which blockchain tokens can be included under the existing German civil law framework of the BGB (German Civil Code). The key question is how goods can be legally represented ("tokenised") digitally and effectively by tokens instead of in documents. There are several approaches to make tokens marketable. Among them are also those that let the "r…

Estimation of leaf area index using PROSAIL based LUT inversion, MLRA-GPR and empirical models: Case study of tropical deciduous forest plantation, N…

2020

Abstract Forests play a vital role in biological cycles and environmental regulation. To understand the key processes of forest canopies (e.g., photosynthesis, respiration and transpiration), reliable and accurate information on spatial variability of Leaf Area Index (LAI), and its seasonal dynamics is essential. In the present study, we assessed the performance of biophysical parameter (LAI) retrieval methods viz. Look-Up Table (LUT)-inversion, MLRA-GPR (Machine Learning Regression Algorithm- Gaussian Processes Regression) and empirical models, for estimating the LAI of tropical deciduous plantation using ARTMO (Automated Radiative Transfer Models Operator) tool and Sentinel-2 satellite im…

Estimating the phenological dynamics of irrigated rice leaf area index using the combination of PROSAIL and Gaussian Process Regression

2021

The growth of rice is a sequence of three different phenological phases. This sequence of change in rice phenology implies that the condition of the plant during the vegetative phase relates directly to the health of leaves functioning during the reproductive and ripening phases. As such, accurate monitoring is important towards understanding rice growth dynamics. Leaf Area Index (LAI) is an important indicator of rice yields and the availability of this information during key phenological phases can support more informed farming decisions. Satellite remote sensing has been adopted as a proxy to field measurements of LAI and with the launch of freely available high resolution Satellite imag…

Characterization of a novel open reading frame, urf a, in the mitochondrial genome of fission yeast: correlation of urf a mutations with a mitochondr…

1991

Between the genes for tRNA(gin) and tRNA(ile) an open reading frame of 227 amino acids has been identified which is unique among known mitochondrial genomes and which has been termed urf a (Lang et al. 1983; Kornrumpf et al. 1984). It uses the "mitochondrial" genetic code, i.e., it contains a TGA codon, whereas all other protein-encoding genes, and all but one intronic open reading frame, use the "standard" genetic code (UGG for tryptophan). A previous paper has demonstrated that "mutator" strains show an increased formation of mitochondrial drug-resistant and respiration-deficient mutants (including deletions). In this paper we show that the mutator activity is correlated with mutations in…

Gray code for permutations with a fixed number of cycles

2007

AbstractWe give the first Gray code for the set of n-length permutations with a given number of cycles. In this code, each permutation is transformed into its successor by a product with a cycle of length three, which is optimal. If we represent each permutation by its transposition array then the obtained list still remains a Gray code and this allows us to construct a constant amortized time (CAT) algorithm for generating these codes. Also, Gray code and generating algorithm for n-length permutations with fixed number of left-to-right minima are discussed.