October 11, 2017   |   Use Case

The main bottleneck in genomic analysis is the shift from data generation to data interpretation. Primary level of genomic analysis such as quality control, read mapping and de novo assembly can be executed with ease, but secondary analysis which involved data mining and exploration are time-consuming, required specialised tools, and deep interpretation.

Flexible visualisation tools, which illustrate the data from secondary analysis to ease interpretation, will be a powerful driving factor in the future of DNA sequencing and “omics” analysis. Arkgene strives to be the main hub for hosting various visualisation tools for the analysis of bacterial genome.

As an example, a researcher has sequenced the genome of melioidosis-causing bacteria Burkholderia pseudomallei. By using bioinformatics tools, he/she has predicted the structural genes (e.g. tRNA and rRNA) and functional genes (e.g. protein-coding), and then annotated them against GO, KEGG, Interpro, Signal Peptide and Transmembrane databases.

The genome sequence and predicted genes were saved in Fasta file while the annotated information were embedded in one or more Microsoft Excel files. This limits the data analysis and interpretation. Also, it challenges the “imagination” of the researcher to bring the B. pseudomallei genome and its annotations into one big picture.

With Arkgene, he/she can browse his/her B. pseudomallei genome using CGbase genome browser, which align the reference genome with gene models and annotations side by side, enabling quick overview of the genome map. The researcher can also zoom into individual gene model, view the gene information (such as sequence start and stop, chromosome number and source of annotation) and extract the whole gene/transcript sequence, or specific region within the gene.

In addition, the researcher can easily generate a publication-ready circular map image using ClicO FS tool (doi.org/10.1093/bioinformatics/btv433) that is already integrated into the Arkgene platform, allowing interactive presentation in scientific papers, reports, and materials for seminars and conferences.

With all these visualisation tools, the researcher can offload his/her headache (e.g. viewing the whole genome or plotting the genome map) to Arkgene, and focus more on data analytics, research discovery, interpretation and findings.

Arkgene visualisation tools, connecting the dots between data generation and biological interpretation.