Search results for "sequences"
showing 10 items of 359 documents
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
2017
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by a…
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data
2017
AbstractThe epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin…
Variable Ranking Feature Selection for the Identification of Nucleosome Related Sequences
2018
Several recent works have shown that K-mer sequence representation of a DNA sequence can be used for classification or identification of nucleosome positioning related sequences. This representation can be computationally expensive when k grows, making the complexity in spaces of exponential dimension. This issue effects significantly the classification task computed by a general machine learning algorithm used for the purpose of sequence classification. In this paper, we investigate the advantage offered by the so-called Variable Ranking Feature Selection method to select the most informative k − mers associated to a set of DNA sequences, for the final purpose of nucleosome/linker classifi…
dAPE: a web server to detect homorepeats and follow their evolution.
2016
Abstract Summary Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats. Availability and Implementation dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx. Supplementary information Supplementary data are available at Bioinformatics online.
Genome Sequence of Bifidobacterium breve INIA P734 (CECT 8178), a Strain Isolated from Human Breast Milk
2021
Departamento de Tecnología de Alimentos (INIA)
Nearly Complete Genome Sequence of a Human Norovirus GII.P17-GII.17 Strain Isolated from Brazil in 2015
2019
Human noroviruses are the most common cause of nonbacterial acute gastroenteritis worldwide. We report here the nearly complete genome sequence (7,551 nucleotides) of a human norovirus GII.P17-GII.17 strain detected in July 2015 in the stool sample from an adult with acute gastroenteritis in Brazil.
Biomarkers of Oxidative Stress for Neonatal Lung Disease
2021
The transition from prenatal to postnatal life causes a significant increase in arterial oxygen tension and the activation of metabolic pathways enabling the newborn's adaptation to the extra-uterine environment. The balance between pro-oxidant and anti-oxidant systems is critical to preserve cellular functions. Indeed, oxidative stress (OS) occurs when the production of free radicals is not balanced by the activity of intracellular antioxidant systems, contributing to cellular and tissue damage. Perinatal OS may have serious health consequences during the postnatal period and later in life. Namely, OS has been recognized as the major cause of lung injury in newborns, especially those prete…
Chromosomal distribution of interstitial telomeric sequences in nine neotropical primates (Platyrrhini): possible implications in evolution and phylo…
2016
To localize interstitial telomeric sequences (ITSs) and to test whether their pattern of distribution could be linked to chromosomal evolution, we hybridized telomeric sequence probes (peptide nucleic acid, PNA) on metaphases of New World monkeys: Callithrix argentata, Callithrix jacchus, Cebuella pygmaea, Saguinus oedipus, Saimiri sciureus, Aotus lemurinus griseimembra, Aotus nancymaae (Cebidae), Lagothrix lagotricha (Atelidae) and Callicebus moloch (Pithecidae), characterized by a rapid radiation and a high rate of chromosomal rearrangements. Our analysis of the probe signal localization allowed us to show in all the species analysed, as normally, the telomeric location at the terminal en…
Draft genome sequences of Vibrio vulnificus strains recovered from moribund tilapia
2021
Potentially zoonotic Vibrio vulnificus strains were isolated from vibriosis outbreaks occurring on eastern Mediterranean tilapia farms between 2016 and 2019. In this work, the draft genome sequences of three representative isolates are presented.
Charitable food aid in Finland: from a social issue to an environmental solution
2019
Since the establishment of the first food bank in 1995, charitable food aid (CFA) has become entrenched in Finland as a seemingly irreplaceable solution to food poverty. Further, it has recently been suggested that the focus of food aid activities is shifting from food poverty and temporary hunger alleviation towards environmental sustainability through addressing food waste via organized re-distribution of expiring food from retail to charitable organizations. This potentially creates a mechanism that (1) solidifies food poverty and (2) fortifies the paradoxical situation where charitable organizations delivering food aid are dependent on food waste rather than trying to reduce it. To unde…