I want to conduct a study using genomes deposited in databases to perform comparative genomics analyses involving different species. Is it possible to do this with already published genomes from different studies, sequencing methods, and varying quality?
NCBI is building some tools that might help. We have a new Multiple Comparative Genome Viewer (MCGV; https://www.ncbi.nlm.nih.gov/mcgv/) that has limited datasets currently, but you can also visualize genome alignments and gene alignments in our Comparative Genome Viewer (MCGV) and as species-species alignment tracks in our GDV genome browser. Please get in touch using the feedback options on NCBI pages if you want to talk more about what you'd like to do.
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This is a very broad question, and the answer depends on what you aim to get out of it. Yes, you can certainly conduct a comparative analysis with published genomes.
You may have to normalise things like read length and depth. But again, it really depends on what you aim to achieve. What is the focus of the project?
I'm new with genomics, I always deal only with molecular evolutionary studies involvieng few genes. So in these cases, I took tens of different genes for tens of different species and analyze their evolutionary aspects, including phylogenetic history (including Baysian inference), selection tests and phylodynamics. So, the project focus is understand the evolutionary history behind the paternal care in Mammalia, using genomic data. But I want know in which extension is possible to do this with public genomic data deposited in data bases.
There are a lot of things to unpack here. But I would say the best course of action is to find genomic studies that do similar things with other traits and try to use some of their workflow. Expanding from gene-based to genomic trait-based comparative genomics is quite a big one in terms of complexity. The difficulty will arise when you start to incorporate genomes that have major differences.
For me, I would probably start with an whole genome alignments, orthology assignment, and then an anchored synteny analysis as a minimum to make comparisons possible. Do you have an academic supervisor for this project?
I appreciate your advice. I have a supervisor, but he doesn't work in this field. This project is something personal that I want to develop because I really like this area and want to improve my skills in Phylogenomics. However, since I don't have the resources to work in this field, I thought about doing something with already published data.
And what do you hope to get out of such a study?
For prokaryotic genomes you will have tens of choices for common organisms. With eukaryotic species your choice is going to be limited. Start here: https://www.ncbi.nlm.nih.gov/datasets/genome/
The same in dthorbur answer.