Mots-Clés

Pangenome, Genome Browser, Hepatitis viruses

Description

Title: Development of Pangenome Browser dedicated to HBV genome diversity.

Background:

The Hepatitis B Virus has a circular DNA genome expressing 8 major viral RNAs (preC, pgRNA, preS1, preS2, S, L-HBx, HBx and S-HBx) and 22 spliced variants (20 deriving from pgRNA, 2 from preS1). Today, 10 genotypes have been described (McNaughton et al., 2020), and the HBVdb (Hayer et al., 2013, https://hbvdb.lyon.inserm.fr/HBVdb/HBVdbIndex) contains 10,041 distinct virus sequences so far.

Recent advances in genomics, powered by computational algorithmic innovations in graph theory, now enable the integration of genetic information into efficiently manageable and queryable pan-genomes. This has led to the creation of bioinformatics tools capable of addressing complexities in genomes. Graph-based pan-genomes can be an elegant solution, integrating all the genetic diversity of HBV, to overcome challenges posed by the absence of a universal reference sequence and the exploitation of disparate -omics data. The resulting tools aim to foster harmony and synchronize acquired knowledge, improving research outcomes in the field of HBV.

Objective:
The goal of this project is to develop a web-based pangenome browser for Hepatitis B Virus. This work will include the production of the pangenome itself, and the development and deployment of a web-based interface to explore and exploit the information of the pangenome.

Required or desired skills :

Knowledge in pangenomics,

Programmation skills (python & R),

Ease of use in a UNIX environment including bash,

Web development skills is a plus.

The student will join the bioinformatics team, they will attend weekly team meetings and will have the opportunity to present their work at those meetings.

Languages: English (mandatory), French (greatly appreciated but not mandatory).

Home-office: Not applicable. Candidate will have to be located or relocate in Lyon area.

References:

Hayer, J., Jadeau, F., Deléage, G., Kay, A., Zoulim, F., Combet, C., 2013. HBVdb: a knowledge database for Hepatitis B Virus. Nucleic Acids Research 41, D566–D570. https://doi.org/10.1093/nar/gks1022

McNaughton, A.L., Revill, P.A., Littlejohn, M., Matthews, P.C., Ansari, M.A., 2020. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. J Gen Virol 101, 271–283. https://doi.org/10.1099/jgv.0.001387