Question: Package for custom visualization of multiple sequence alignment
0
gravatar for tim.ivanov.92
12 months ago by
tim.ivanov.920 wrote:

Is there a package to make custom visualization of multiple sequence alignments?

Specifically, i want to color some exons on a DNA alignment, knowing on their coordinates

visualization msa • 219 views
ADD COMMENTlink modified 12 months ago by ulrich.bodenhofer20 • written 12 months ago by tim.ivanov.920
Answer: Package for custom visualization of multiple sequence alignment
1
gravatar for ulrich.bodenhofer
12 months ago by
Austria
ulrich.bodenhofer20 wrote:

I do not know of a special R package. However, the 'msa' package's msaPrettyPrint() function provides access to all functionality of the TeXshade package via the 'furtherCode' argument. See the package vignette for a basic example (cf. p. 37). I hope that helps.

ADD COMMENTlink written 12 months ago by ulrich.bodenhofer20

thank you for the answer - this package looks quite all right, although i don't see in your example how can i actually access a single line in the alignment: it seems all i can do with this package is apply existing functions to regions inside an alignment, which is not quite my goal

ADD REPLYlink modified 12 months ago • written 12 months ago by tim.ivanov.920
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