Question: Can i use ucsc track browser without a reference organism?
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gravatar for tim.ivanov.92
8 months ago by
tim.ivanov.9210 wrote:

Can i access ucsc *.BED track visualization instrumental for my own alignment file?

This is very weird question, but i can't find any tool, for adding tracks on multiple alignment file. I have a standard clustalw alignment file for ~21 organism. And each of these organism has some features, which i want to see on my alignment.

So what i've thought of for now is just create a .BED file with my features coordinates, and then upload it to genome browser. Can i use it without any special organism as reference, though?

ucsc clustalw annotation aln • 298 views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 8 months ago by tim.ivanov.9210
1

I don't think you can do that. You're looking for a MSA visualization tool, not a track browser.

ADD REPLYlink written 8 months ago by RamRS21k
1

Here are 2 MSA visualisation tools: MSAViewer and Wasabi

Here are 2 R packages doing a little more: MSA (Bioconductor) and Balcony (Cran)

But could we get some detail on what "features" you are trying to view/compare?

ADD REPLYlink modified 8 months ago • written 8 months ago by YaGalbi1.4k

Thank you for your links - i'll definitely look into it!

My features are two lists of exons - one from annotation, and one from my predictions. I want to see their intersection and visualize them

ADD REPLYlink written 8 months ago by tim.ivanov.9210

If you simply want to make a pretty picture of the comparison, then try IBS Illistrator

Also see this list of alignment visualisation software

ADD REPLYlink written 8 months ago by YaGalbi1.4k

thank you for your reply, but it looks like IBS is only a manual draw tool - which is not uncomfortable for drawing ~ 50 organisms, each having ~ 20 features

from that list - i've seen a few, but none of them seems to have an option of importing users features Can you point me on a tool that can, if you know any?

ADD REPLYlink modified 8 months ago • written 8 months ago by tim.ivanov.9210
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