L A TEX Tools for Life Scientists ( BioTEXniques ? )

LTEX has been a long time favorite of mathematicians and physicists alike. However now, many packages are available, that have tremendously extended the capabilities of LTEX beyond routine typesetting and provide biologists new avenues to not only typeset documents, but also help in the visualization of membrane proteins and in the analysis of DNA or amino acid sequences by multiple sequence alignment. I will discuss with examples some of the LTEX packages and tools that are presently available for the biologists. Scientific journals (for biological research) now accept TEX/LTEX formatted manuscripts, although they are still a rarity. This article will provide the references of those sources that might be helpful to prospective authors from life sciences that want to submit manuscripts in TEX/LTEX format. This article is written in the perspective of a biologist who might be interested in creating better documents using LTEX & friends. “Uncle Cosmo . . . why do they call this a word processor?” “It’s simple, Skyler . . . you’ve seen what food processors do to food, right?” – Jeff MacNelly, “Shoe” The advantages of LTEX over WYSIWYG applications are well known 1. It has not only been the traditional application of choice to typeset mathematical formulae, but also had been employed to typeset music scores, games like crossword, chess and bridge. In this article, I will explain some of the tools that can be effectively used by life scientists for preparing documents in LTEX, briefly explain about two LTEX packages related to biology namely, TEXshade and TEXtopo, developed by Eric Beitz, discuss about XFig and Inkscape, two well known drawing programs and also give some examples illustrating the use of XyMTeX, a package for drawing chemical structures. I will end my article with some references to online sources that might be helpful to life science researchers in search of a style file or a bibliography file suitable for a particular journal and other LTEX sources. Regular readers of this journal would have read an earlier article by Peter Flom[1]. It is one of the good places to start for academicians with little or no LTEX experience, since it provides a good introduction and shatters several myths about LTEX. The present article is written to help mainly biochemists and molecular biologists. A general background on using TEX or LTEX would be useful, but not essential to try the things described in this article. 1. For example: http://nitens.org/taraborelli/latex and links therein. Copyright © 2007 Senthil Kumar M. Permission is granted to distribute verbatim copies of this document provided this notice remains intact. 1 Importance of multiple sequence alignment Proteins are polymers of amino acids and they form the building blocks of life. Enzymes that catalyze the chemical reactions in our cells, hemoglobin that carriers oxygen to our cells through bloodstream, actin that provides stability to cells are some examples of proteins. Proteins are encoded by specific genes. Information in DNA (in the form of 4 letters: A or T or G or C) are translated into amino acids (20 different letters) during protein synthesis. Therefore, analyzing DNA or protein sequences is pivotal to determine the nature of how genes and thus proteins have changed during evolution. Aligning multiple sequences of either DNA or protein sequences from many different organisms is called as multiple sequence alignment. It provides an overall view of comparative changes in the sequences under study, that may have occured due to mutations. 1.1 Aligning sequences using TEXshade Availability: CTAN Author: Eric Beitz Current Version : 1.17 TEXshade, a LTEX package provides an ideal solution of displaying the key changes in DNA (4 letters: A, T, G and C) or protein (20 different amino acids, indicated by unique single letters) sequences with great control. Other programs do exist that provide a way to display sequence similarities in multiple sequence alignment prettyplot2, included in EMBOSS3, a open source software for molecular biology), is one good example. However, only TEXshade provides: – LTEX quality output. – Flexibility: The alignments can be typeset as per the needs for example, while writing a paper using LTEX. TEXshade provides different modes of shading, therefore, it takes less time to modify an alignment. DNA or Protein sequences are aligned a priori using alignment programs like clustalW to generate an output file (usually a plain text ASCII file) containing the alignment of sequences from different species. TEXshade can then be used to highlight the level of similarity/identity/dissimilarity among the sequences. TEXshade provides four predefined shading modes: identity, similarity, diversity and functionality. They come useful depending on what one requires. For example, if one would like to determine the sequence similarity (as shown in Figure 1), similar option highlights the residues that are similar in all the species. If one is interested in showing 2. http://bioweb.pasteur.fr/docs/EMBOSS/prettyplot.html 3. http://emboss.sourceforge.net/