Sachithra Kalhari Yaddehige
Education:
BSc Eng (Hons) in Biosystems Engineering, Asian Institute of Technology, Thailand
MSc in Biotechnologies for food science, University of Padova, Italy
Research areas:
Bioinformatics
Brief descrition of the P.h.D project:
Developing and maintaining a software tool and an online database called the genome-based retrieval and analysis parser (GBRAP). The tool was developed in Python 3. It is able to parse GenBank files (GBFF format) and generate a diverse range of genomic data, from small genomes like those of bacteria and viruses to larger ones belonging to amphibians, plants, and mammals. Moreover, it generates these data for each chromosomal, mitochondrial, plastid, or plasmid sequence separately (where applicable).
The data generated by GBRAP was used to build an online database (http://tacclab.org/gbrap/). The database, accessible without any registration, houses datasets for more than 49,000 organisms and includes metrics such as base composition, GC content, entropy measures, codon usage, and adherence to Chargaff's second parity rule. These data are available not only for whole sequences but also for distinct genomic elements, such as introns, tRNA, rRNA, and ncRNA. The full paper is available at Molecular Biology and Evolution at https://doi.org/10.1093/molbev/msaf114.
Supervisor and co-supervisor:
Prof. Cristian Taccioli
Prof. Rebecca Ricci
Publications:
https://orcid.org/0009-0004-6809-6720
Contacts:
