Is it enough to find a transgene sequence in the genetically engineered bacteria (via BLAST server) to confirm that the engineering was successful? In general, how to prove that genetic engineering was successful by using bioinformatics tools? Is the phylogenetic tree would be recommended? What else could you suggest?
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linas.kapocius •
If you are engineering a bacteria, you are probably working with a single-isolate culture. Then, the complete workflow would be: sequence the original strain, sequence the putative transformed strain - best to sequence both with PacBio or Nanopore, assemble both genomes. Then there is a number of analyses you should perform: align the genomes, search the transgenes in both genomes (with Blast or other program), check if the transgene is complete, if the marker gene (if any, e.g., some antibiotic resistance gene) is present, and so on.
If you are engineering an eukaryote, you can follow the same workflow, but the more complex the genome (e.g., some polyploid plants), the more difficult will be to fully characterize the transgene (where it inserted, how many copies, if it integral or not, etc). In this case, wet lab techniques can be faster and cheaper than sequencing plus bioinformatics.
Horizontal gene transfer is common in bacteria:
https://en.wikipedia.org/wiki/Horizontal_gene_transfer
thus just finding a new gene in a bacteria would not be indicative of genetic engineering.
What I would say here, is that if you find an "interesting" transgene sequence in a bacteria, that is really out of place and makes no sense, and depending on what that gene is and how it fits with the rest, you could explore the possibilities there.
After all, bacteria are the easiest organisms to manipulate in labs.
In my not-so-well-informed opinion, an analogy would be that bioinformatics is still working on confidently removing typos and what you're asking it is akin to the job of a newspaper editor. No matter what bioinformatics says, wet bench research is required to back it up. With that level of questioning, where we can only say with a certain amount of confidence if something we see if real, how can bioinformatics be expected to predict who created that reality?
It is an interesting question, with many complex answers. While there may not be a singular, foolproof way to tell that, depending on the particular case, there could be hints that could indicate genetic engineering.
how to prove that genetic engineering was successful by using bioinformatics tools?
What experimental data you are going to apply bioinformatics tools to? RNAseq (to show that the gene is expressed) or DNAseq (to show that the gene is present without being able to say if it is working)? Bioinformatics is only providing tools. You will still need to design/think of a proper experiment to apply the right tools. You may be able to get by without bioinformatics if there is a phenotype/growth characteristic you can easily monitor.
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Unfortunately, I disagree.
If it is not a bioinformatics-related question, please, tell me where to ask? How to analyze a genome of an organism without bioinformatics tools? I am thinking about the blast and phylogenetic tree, but I want to know the experts' opinions... What is wrong with that?
In general I would recommend the following:
Try to ask precise question. If you have a certain analysis in mind and get stuck at some point towards bioinformatics then try to describe the problem in detail. Open-ended questions like this one are generally not appreciated simply because it takes a lot of effort to even find out at which point you get stuck. The problem that "made in the lab" questions often create is that it sounds like a conspiracy theory, if you intend that or not (probably you didn't). Therefore, I would simply describe your analysis and where you get stuck, from a technical perspective, in detail. If you want to do that you can use the
editfunction to change your question, we might then reopen it, but in its current form, after discussing with other moderators, it will remain closed.Hello linas.kapocius!
We believe that this post does not fit the main topic of this site.
I have got an answer
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
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