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So I am using Texshade to show similarities in a MSA (Multiple sequence alignment). I am mostly interested in the alignment of the CpG sites (i.e. where the CG pair of nucleotide). I am not sure how to go about displaying the MSA with only the CG pairs highlighted. I have tried using the \DNAgroups command with {CG} but this does not seem to work. If anyone has any suggestion on how to do this that would be very much welcomed. Here is my current .tex file:

\documentclass[10pt]{article}

\usepackage{times}
\usepackage{texshade}

\headheight=0pt
\headsep=0pt
\hoffset=0pt
\voffset=0pt
\paperwidth=11in
\paperheight=8.5in
\ifx\pdfoutput\undefined
\relax
\else
\pdfpagewidth=\paperwidth
\pdfpageheight=\paperheight
\fi
\oddsidemargin=-0.9in
\topmargin=-0.7in
\textwidth=10.8in
\textheight=7.9in

\pagestyle{empty}

\begin{document}
\begin{texshade}{./myFile.fasta}
\seqtype{N}
\shadingmode{similar}
\DNAgroups{CG}
\threshold{50}

\showconsensus[ColdHot]{bottom}

\shadingcolors{blues}

\hidelogoscale

\shownames{left}

\end{texshade}
\end{document}

Another remark: I am using the R package msa is create this .tex file.

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1 Answer 1

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enter image description hereThe best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this:

\shaderegion{1}{CG}{Red}{OrangeRed}

\shaderegion{2}{CG}{Red}{OrangeRed}

...

Then I cast the rest of shading similarity to grey so the CG pairs were more easily distinguishable.

\shadingcolors{grays}

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