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6 weeks ago
gokberk ▴ 70

Miropeats download link seems not to work, I keep receiving an error saying The requested URL was not found on this server. when I go to this link. So I was wondering if it works for other people or if anyone knows of an alternative way to download this? I looked for a github repo for miropeats but could not find one. Thanks in advance!

miropeats • 454 views
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That looks like a 25+ year old software. You may be better off using something current. What is it that you wanted it for?

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It is indeed very old, but I guess most of such sequence alignment tools were developed in '90s, right? I want to have a look at the overall genetic structure of a GWAS hit locus. I already have a LocusZoom plot, but I would like to see if there are any large duplications, inversions etc. around this site. I was hoping to have something like panel A below:

I think any proper sequence alignment visualization tool would do it, but I'm not aware of a recent good one. Happy to hear any suggestions! :)

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What format is your input/aligned data in?

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Fasta of a region from hg38, I was planning to self-align it and look for duplications etc. Then I will crop out the corresponding region from the chimp genome (again fasta). Alignment is a bit tricky as it is a largely intergenic region though. So I want to see if there are any intergenic bits that are conserved.

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You could give mauve (LINK) a try for start.

Plot type you show above are referred to as alluvial plots. You will need to find a way to transform your alignments into something that you can use to plot.

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I will have a look at mauve, many thanks for your help! There are a couple of other alternatives in this previous post as well if people are interested.

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gggenomes seems very useful too.