I have to do the comparative genomics of the various genomes present on NCBI for Xanthomonas Oryzae species. I am having major issues in that. I don't have any programming experience, per se.
I have been unable to do MSA of these entire genomes, even after trying in batches of 20. All the online tools show some or the other error. Even if I just take the 96 complete genomes, I don't have any tools to compare them with each other. My end aim is to do the comparative genomics of such species to find the signature proteins for the virulence genes and then compare my results with the literature present on them.
However, I am unable to even reduce this genome dataset to an exhaustive one and have been stuck since weeks on this. Kindly help me on how to go about this project. Even BLAST-N results aren't coming for these genome comparisons. I have hit a dead end early on itself.
Thank you
Phylogenomics is the answer. If you do not know how to write your own code, thats perfectly fine, however, without the knowlegede of basic CLI usage, the task you mention seems difficult. There are tools for the task, but they are mostly availble for the command line usage. Apart from that, undergoing such huge study requires sound knowledge of comparative genomics and phylogenomics.
First, it appears that you are trying to do your alignments by searching online genome databases. This will not work. However, it is very easy to run whole genome x whole genome blast searches using blast installed on a standard laptop (ideally running unix or linux). Most importantly, however, you will need to learn programming (python) to interrogate the blast reports, as well as learn how to navigate the command line.
You should focus on the most important elements of your genomes. These are often the orthologous genes. These can individually be aligned and then concatenated. There are several pipeline for this purpose, one is Roary https://sanger-pathogens.github.io/Roary/
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