Comparative genomics software


(James McKay) #1

Seeing the recent discussions that have started up about AiG’s discussions about genetics (here and here), there’s one thing that I think both sides in the debate are missing.

The genomes under discussion are available for free download from the Internet, and the programs to compare them are open source. This means that it should be possible for anyone who is interested to be able to actually explore the sequences and fact-check the respective claims for themselves.

Unfortunately, I haven’t seen much in the way of guidance on how to use these programs. I tried running a couple of sequences through a web-based BLAST implementation a while back, but I was a bit mystified about how to interpret the results.

It would be good if we could have a series of blog posts or tutorials here on the BioLogos website on how to use these tools and what to look out for.

Is anyone with the necessary expertise able to oblige?


#2

I think that @DennisVenema would be just the person to ask.


(James McKay) #3

Quite possibly yes. I was also thinking of @Swamidass – I know he specialises in computational biology in particular, and he seems to be especially knowledgeable about that side of things.


#4

My expertise doesn’t include large scale genomic alignments, but one of the tools I have found handy for local alignments and general info is www.Ensembl.org. For example, you can go to the page for the human gene for MMP9. There is a box on the top left hand side of the web page for all sorts of comparisons, such as genomic alignments, ortholgues, paralogues, primary sequence, and variants. If you click on the sequence option you are sent to a page where it gives you an option to BLAST the entire gene against other genomes. On subsequent pages you can select which species you want to search against, and you can also opt to use a BLAT search which is a lot faster than a BLAST search.

If you are into such things, you can find yourself going down the internet rabbit hole exploring all of the functions that Ensembl has. I’m not sure if Ensembl is what you are looking for, but it is a useful tool for comparing limited regions for multiple multiple species.

UCSC Genome Browser is another popular database:
https://genome.ucsc.edu/cgi-bin/hgGateway


(James McKay) #5

Thanks for the heads-up about Ensembl and the UCSC Genome Browser. I’d already come across these particular sites – in fact I did mention that I’d tried one of them out on one occasion, though I can’t remember exactly which one.

My big problem though is not where to find them, but how to use them and how to interpret the results. I’m not a geneticist and consequently I found them a bit cryptic. But the other thing is that I see their potential for providing evidence that anyone can explore when considering the whole issue of evolution. The vitellogenin genes, for example – where are they, what do they look like, how can we find them, and how can we see for ourselves which bits are the same and which bits have changed? That’s why I’d welcome a blog series on how they work, how to use them and how to interpret their results.


#6

You might want to check out Figure S2 from the vitellogenin pseudogene paper. It has some of the sequence alignment for exon3 of the vit1 gene.


(system) #7

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