Properly Displaying Amino Acid Sequence Using Latex

Question

[Pals]

Hi, I am trying to show/write the protein sequence using latex. I tried to do it normally (as a paragraph), using makebox, and boxedminipage but none of those were able to show the sequence normally. There were extra gaps introduced within the sequence or it ran out of the border. Could anyone tell me how I can get rid of this problem.

Thanks.

[Neilfws]

Related: http://biostar.stackexchange.com/questions/12176/favorite-sequence-layout-typesetting-in-latex

Answer 1

[Frédéric Mahé]

Maybe the TeXshade package is what you're looking for? I quote the package description:

TeXshade is alignment shading software completely written in TeX/LaTeX; it can process multiple sequence alignments in the .MSF and the .ALN file formats. In addition to common shading algorithms, it provides special shading modes showing functional aspects, e.g. charge or hydropathy, and a wide range of commands for handling shading colours, text styles, labels, legends; it even allows the user to define completely new shading modes.

It processes multiple alignments,but it also works for single sequences.

Answer 2

[Martin A Hansen]

I remember a section on this in The LaTeX companion.