Biology subjects

Vieira, F. R. J.

Publications and source records attributed to Vieira, F. R. J..

3 recordsLinked to original sources

bioRxiv2021

DAVI: a tool for clustering and visualising protein domain architectures

The characterization of protein functions is one of the main challenges in bioinformatics. Proteins are often composed of individual units termed domains, motifs that can evolve independently. The domain architecture of a given protein is the particular order and the content of its numerous domains. Some computational approaches predict the most likely domain architecture for a set of proteins. However, a few numbers of visualization tools exist, and most of them are unavailable. Here we present DAVI, an efficient and user-friendly web server for protein domain architecture clustering and visualization. DAVI accepts the output of most used domain architecture prediction tools and also produces domain architectures for a set of protein sequences. It provides a rich visualization for comparing, analyzing, and visualizing domain architectures. Availabilityhttp://genome.lcqb.upmc.fr/Domain-Architecture-Viewer

bioinformatics↗

bioRxiv2019

H3K27me3 natural variation selectively marks genes predicted to be important for differentiation in unicellular algae

O_LIIn multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit H3K27me3 to establish and maintain gene silencing, critical for developmentally regulated processes. PRC2 complex is absent in both widely studied model yeasts which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. C_LIO_LIHere, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di and tri-methylation of lysine 27 of histone H3. C_LIO_LIH3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. C_LIO_LIThese results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species and highlight their ancestral function in a broader evolutionary context than is currently appreciated. C_LI

cell biology↗

bioRxiv2019

2dSS: a web server for protein secondary structure visualization

2dSS is a web-server for visualising and comparing secondary structure predictions. It provides two main functionalities: 2D-alignment and compare predictions. The \"2D-alignment\" has been designed to visualise conserved secondary structure elements in a multiple sequence alignment (MSA). From this we can study the secondary structure content of homologous proteins (a protein family) and highlight its structural patterns. The \"compare predictions\" has been designed to compare the output of several secondary structure prediction tools, and check their accuracy when compared with real secondary structure elements extracted from 3D-structure. 2dSS provides a comprehensive representation of protein secondary structure elements, and it can be used to visualise and compare secondary structures of any prediction tool.\n\nAvailabilityhttp://genome.lcqb.upmc.fr/2dss/

bioinformatics↗