Work

PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era

Year: 2024

Type: article

Abstract: Summary: High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic mutational events such as premature stop codons, deletions and insertions. It enables the investigation of cross-species genomic datasets through: (i) integration into automated workflows, (ii) multiprocessing capability, and (iii) creation of a functional reference from annotation files. In addition, we introduce PseudoViz, a novel graphical interface designed to help interpret the results of PseudoChecker2 with intuitive visualizations. These tools combine the versatility and automation of a command-line tool with the user-friendliness of a graphical interface to tackle the challenges of the Genome Era. Availability and implementation: PseudoChecker2 and PseudoViz are fully available at https://github.com/rresendepinto/PseudoChecker2and https://github.com/rresendepinto/PseudoViz.

Source: Bioinformatics Advances

DOI: 10.1093/bioadv/vbaf202

Authors: Rui Resende-Pinto, Raquel Ruivo, Josefin Stiller, Rute Fonseca, Luís Filipe C Castro

Institutions: Universidade do Porto, Centro Interdisciplinar de Investigação Marinha e Ambiental, University of Copenhagen

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,917

Funder: Villum Fonden