Hi all,
Using polyphasic approach, I found out a novel species of bacteria. I want to delineate this species futher in the basis comparative genomics.
Can you suggest some methods which can be used easily (web-based interface) + which allows users to to upload their own sequenced genome?
Regards,
Timsy
P.S: I am aware of EDGAR, any other?
The 16S ribosomal RNA (or genes that encode them) sequences will be the best for identifying your organism. The rest of the genome may also be useful for further identification, but 16S rRNA will get you to a species level identification most rapidly.
http://www.cbs.dtu.dk/services/RNAmmer/
https://www.arb-silva.de/
https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/21/rrna-databases/
Apart from 16s, you can also check for phylogenetic analysis using the rpoB gene.
https://currents.plos.org/treeoflife/index.html%3Fp=385.html
Dear Timsy --
In terms of comparative genomics, you could use an approach based on the Average Nucleotide Identity (ANI) between the genome of the species you are working with and a set of reference genomes. There are different tools, such as:
pyani: https://github.com/widdowquinn/pyani
FastANI: https://github.com/ParBLiSS/FastANI
Mash: https://mash.readthedocs.io/en/latest/index.html
Briefly, the first mentioned two tools align your genome with the other reference genomes in order to obtain the average nucleotide identity/similarity (ranges between 0-100%). The last tool, Mash, uses a kmer-based approach and gives you a metric called "distance" (ranges between 0-1). A distance of 0 means that the genomes are exactly the same, a distance of 1 means that the genomes have nothing in common. The Mash distance metric is usually used to create phylogenetic trees from whole-genome comparisons. Nevertheless, these tools have to be executed via command-line in Linux.
An online alternative that uses Mash is PATRIC: https://www.patricbrc.org/app/GenomeDistance. You can upload your genome in FASTA format and you will know the closest genome and the Mash distance metric.
Hope it helps.
Best regards,
Andreu Paytuví-Gallart
Bioinformatician @ www.sequentiabiotech.com
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