Favorite Sequence Layout/Typesetting In Latex

Question

[Fabian Bull]

A friend of mine (he is a physicist) just asked me if I have a standard way of texing DNA sequences. I do not have one but was curious for a good solution.

Anyone has a good solution to this? It should have publication quality. Coloring and marking specific subsequences should be possible.

If you have one not using LaTex: Feel free to add.

Answer 1

[Laurent]

From the TeXshade README file: TeXshade is an alignment shading software completely written in TeX/LaTeX which can process multiple sequence alignments in the MSF, ALN and FASTA file format.

I have happily used it in the past, although large alignments were likely to cause issues (but that was many years ago).

Answer 2

[Martin A Hansen]

I am pretty sure alignments are covered in the LaTeX companion, however, it's been a few years and I could be wrong. Personally I would avoid LaTeX for this (too complicated) and simply render sequences in SVG.

[Fabian Bull]

There are nice packages for alignments but I am not looking for alignments.

Answer 3

[Neilfws]

I don't believe there is a standard solution, or very many packages aimed at sequence formatting in LaTeX. Most people would roll their own, using their knowledge of LaTeX.

This is a few years old but might be useful for other purposes:

LaTeX Tools for Life Scientists (PDF)