On the Identification of Clinically Relevant Bacterial Amino Acid Changes at the Whole Genome Level Using Auto-PSS-Genome

• Type: Article in International Scientific Journal
• Date: 2021

Authors

Lopez Fernandez, H (Author) Other; Cristina Vieira (Author) FCUP; Ferreira, P (Author) Other; Gouveia, P (Author) Other; Fdez Riverola, F (Author) Other; Reboiro Jato, M (Author) Other; Vieira, J (Author) ICBAS

Journal

Title: Interdisciplinary sciences, computational life sciences

Vol. 13

Pages: 334-343

ISSN: 1913-2751

Publisher: Springer Nature

Indexing

ISI Web of Knowledge - 1 Citation

Scopus - 1 Citation

Other information

Authenticus ID: P-00T-Z7R

DOI: 10.1007/s12539-021-00439-2

Abstract (EN): The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively selected amino acid sites (PSS). Nevertheless, such analyses are time consuming, and the frequency of genes showing evidence for PSS can be low. Therefore, the development of a pipeline that allows the quick and efficient identification of the set of genes that show PSS is of interest. Here, we present Auto-PSS-Genome, a Compi-based pipeline distributed as a Docker image, that automates the process of identifying genes that show PSS using three different methods, namely codeML, FUBAR, and omegaMap. Auto-PSS-Genome accepts as input a set of FASTA files, one per genome, containing all coding sequences, thus minimizing the work needed to conduct positively selected sites analyses. The Auto-PSS-Genome pipeline identifies orthologous gene sets and corrects for multiple possible problems in input FASTA files that may prevent the automated identification of genes showing PSS. A FASTA file containing all coding sequences can also be given as an external global reference, thus easing the comparison of results across species, when gene names are different. In this work, we use Auto-PSS-Genome to analyse Mycobacterium leprae (that causes leprosy), and the closely related species M. haemophilum, that mainly causes ulcerating skin infections and arthritis in persons who are severely immunocompromised, and in children causes cervical and perihilar lymphadenitis. The genes identified in these two species as showing PSS may be those that are partially responsible for virulence and resistance to drugs. [GRAPHICS] .

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 10