Package for custom visualization of multiple sequence alignment
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@timivanov92-14799
Last seen 2.9 years ago

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

MSA visualization • 556 views
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@ulrichbodenhofer-8624
Last seen 2.8 years ago
Austria

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.

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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