Showing papers by "Matej Lexa published in 2015"
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TL;DR: It is emphasized that TEs may serve as vehicles for the genomic spread of G-quadruplexes and these non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.
Abstract: A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.
42 citations
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TL;DR: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters.
Abstract: Motivation: Proteins often recognize their interaction partners
on the basis of short linear motifs located in disordered
regions on proteins' surface. Experimental techniques that
study such motifs use short peptides to mimic the structural
properties of interacting proteins. Continued development of
these methods allows for large-scale screening, resulting in
vast amounts of peptide sequences, potentially containing
information on multiple protein-protein interactions.
Processing of such datasets is a complex but essential task for
large-scale studies investigating protein-protein interactions.
Results: The software tool presented in this article is able to
rapidly identify multiple clusters of sequences carrying shared
specificity motifs in massive datasets from various sources and
generate multiple sequence alignments of identified clusters.
The method was applied on a previously published smaller
dataset containing distinct classes of ligands for SH3 domains,
as well as on a new, an order of magnitude larger dataset
containing epitopes for several monoclonal antibodies. The
software successfully identified clusters of sequences
mimicking epitopes of antibody targets, as well as secondary
clusters revealing that the antibodies accept some deviations
from original epitope sequences. Another test indicates that
processing of even much larger datasets is computationally
feasible.
32 citations
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15 Apr 2015TL;DR: The newly-developed Python library sqlAutoDenorm.py automatically generates SQL commands to denormalize a subset of database tables and their relevant records, effectively generating a flat table from arbitrarily structured data.
Abstract: Relational databases are sometimes used to store biomedical and patient data in large clinical or international projects. This data is inherently deeply structured, records for individual patients contain varying number of variables. When ad-hoc access to data subsets is needed, standard database access tools do not allow for rapid command prototyping and variable selection to create flat data tables. In the context of Thalamoss, an international research project on β-thalassemia, we developed and experimented with an interactive variable selection method addressing these needs. Our newly-developed Python library sqlAutoDenorm.py automatically generates SQL commands to denormalize a subset of database tables and their relevant records, effectively generating a flat table from arbitrarily structured data. The denormalization process can be controlled by a small number of user-tunable parameters. Python and R/Bioconductor are used for any subsequent data processing steps, including visualization, and Weka is used for machine-learning above the generated data.
2 citations