Favorite Sequence Layout/Typesetting In Latex
3
5
Entering edit mode
13.1 years ago
Fabian Bull ★ 1.3k

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.

sequence • 7.0k views
ADD COMMENT
5
Entering edit mode
13.1 years ago
Laurent ★ 1.7k

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).

ADD COMMENT
1
Entering edit mode
13.1 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
13.1 years ago
Neilfws 49k

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)

ADD COMMENT

Login before adding your answer.

Traffic: 1026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6