texshade

A LaTeX package for setting nucleotide and peptide alignments:

Setting alignments of nucleotides and peptides for publication or presentation purposes is usually a time consuming two-step process. First, a scientific software is used for the calculation of the alignment. This is done in a few minutes. Then, in order to highlight special sequence relationships and to label positions and regions of interest a second software with high output capability is needed.

Manipulating sequence alignments with standard word processing or graphics programs takes its time - often several hours - and simple layout changes such as rebreaking lines, say from 50 to 40 residues per line, elongate the working time considerably.

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. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes. TeXshade combines highest flexibility and the habitual TeX output quality - with reasonable time expenditure.

Beitz, E. (2000) TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e. Bioinformatics 16: 135-139. PubMed
Beitz, E. (2006) Subfamily logos: visualization of sequence deviations at alignment positions with high information content. BMC Bioinformatics 7:313. PubMed

 

  • Download the current version of TeXshade incl. documentation.
  • Spanish introduction to TeXshade (contributed by Mikel Egana Aranguren):

  • The Biology WorkBench at the San Diego Supercomputer Center provides a limited web-based version of TeXshade.

  • TeXshade is used by the Structural Alignment Program STRAP by Christoph Gille for the output.
   
  Some example outputs:
   
    align1
   

Basic shading: Identity mode
   
    align8
    Feature lines with bar graphs and color scales
 
   
    align2
    More information: Similarity mode
 
   
    align3
    Sequence differences: Diversity mode
 
   
    align4
    Structure information: Functional mode
 
   
    align5
    Charge distribution: Functional mode
 
   
    align6
    Fingerprinting: Similarity mode
 
   
    align7
    Fingerprinting (charge): Functional mode
 
   
    align9
    Sequence logos
 
   
    align10
    Subfamily logos