Question: Tools for visualizing genome
0
gravatar for arit.mhp
9 months ago by
arit.mhp10
arit.mhp10 wrote:

Hi BioStars, I need to visualize the genome sequence (mitochondrial and whole genome). Is there any tools to visualize the genome sequences. Basically I need to know the position of specially different repeats (Short Tandem Repeat and Long Tandem Repeats). Could you please suggest any tools for that? Thanking you,

With regards, Aritra

genome visualization • 288 views
ADD COMMENTlink written 9 months ago by arit.mhp10

It would be useful if you could please provide additional information such as file format of the genome sequence, did you try anything available on the OmicsTools?

ADD REPLYlink written 9 months ago by Sej Modha3.6k

Aritra,

We would need more information to help you. Do you have the positions of the STRs or you need to compute them? As I understand your questio, you don't actually need to visualize the sequence, isn't it?

If you have the positions of the STR's in a BED file or similar, you can use karyoploteR to create the plot. You can find some more information in the tutorial and examples page.

ADD REPLYlink written 9 months ago by bernatgel1.2k

IGV and find motif function would be a fast insight.

ADD REPLYlink written 9 months ago by Buffo1.1k
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