Search results for "030302 biochemistry & molecular biology"
showing 10 items of 238 documents
Evagination of Cells Controls Bio-Silica Formation and Maturation during Spicule Formation in Sponges
2011
The enzymatic-silicatein mediated formation of the skeletal elements, the spicules of siliceous sponges starts intracellularly and is completed extracellularly. With Suberites domuncula we show that the axial growth of the spicules proceeds in three phases: (I) formation of an axial canal; (II) evagination of a cell process into the axial canal, and (III) assembly of the axial filament composed of silicatein. During these phases the core part of the spicule is synthesized. Silicatein and its substrate silicate are stored in silicasomes, found both inside and outside of the cellular extension within the axial canal, as well as all around the spicule. The membranes of the silicasomes are inte…
NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning
2020
© 2020 Rathore et al. This article is distributed exclusively by the RNASociety for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
Traitpedia: a collaborative effort to gather species traits
2018
Abstract Summary Traitpedia is a collaborative database aimed to collect binary traits in a tabular form for a growing number of species. Availability and implementation Traitpedia can be accessed from http://cbdm-01.zdv.uni-mainz.de/~munoz/traitpedia. Supplementary information Supplementary data are available at Bioinformatics online.
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
2018
Abstract Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance perf…
TiFoSi: an efficient tool for mechanobiology simulations of epithelia
2020
[Motivation]: Emerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses.
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
2021
[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
NeoFox: annotating neoantigen candidates with neoantigen features
2020
Abstract Summary The detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features. Availability and implementation NeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox. Supplementary information Supplementary data are available at Bioinformatics online.
Basic networks: Definition and applications
2009
7 pages, 4 figures, 1 table.-- PMID: 19490867 [PubMed]
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures
2020
Abstract Motivation Mash is a popular hash-based genome analysis toolkit with applications to important downstream analyses tasks such as clustering and assembly. However, Mash is currently not able to fully exploit the capabilities of modern multi-core architectures, which in turn leads to high runtimes for large-scale genomic datasets. Results We present RabbitMash, an efficient highly optimized implementation of Mash which can take full advantage of modern hardware including multi-threading, vectorization and fast I/O. We show that our approach achieves speedups of at least 1.3, 9.8, 8.5 and 4.4 compared to Mash for the operations sketch, dist, triangle and screen, respectively. Furtherm…
Synthesis of tritiated derivatives of the diphenylether herbicides acifluorfen and acifluorfen methyl
1992
Acifluorfen 1 and acifluorfen methyl 2, two herbicides of the diphenylether family, are inhibitors of protoporphyrinogen oxidases. Two tritiated derivatives of these compounds, namely 3-[3H]-5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid [3H]-1, and methyl 3-[3H]-5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid [3H]-2, have been synthesised from 3-[3H]-5-hydroxybenzoic acid, in order to probe their interactions with the target enzymes.