T(E)Xshade: Shading and labeling of multiple sequence alignments using L(A)T(E)X2ε

Abstract

Motivation: Typesetting, shading and labeling of nucleotide and peptide alignments using standard word processing or graphics software is time consuming. Available automatic sequence shading programs usually do not allow manual application of additional shadings or labels. Hence, a flexible alignment shading package was designed for both calculated and manual shading, using the macro language of the scientific typesetting software L(A)T(E)X2ε. Results: T(E)Xshade is the first T(E)X-based alignment shading software featuring, in addition to standard identity and similarity shading, special modes for the display of functional aspects such as charge, hydropathy or solvent accessibility. A plenitude of commands for manual shading, graphical labels, re-arrangements of the sequence order numbering, legends etc. is implemented. Further T(E)Xshade allows the inclusion and display of secondary structure predictions in the DSSP-, STRIDE- and PHD-format. Availability: From http://homepages.uni-tuebingen.de/beitz/tse.html (macro package and on-line documentation) Contact: eric.beitz@uni-tuebingen.de.