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Bioinformatics Vol. 16 no. 2 2000
Pages 135-139
© 2000 Oxford University Press
TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e
1 Faculty of Chemistry and Pharmacy, University of Tübingen, Morgenstelle 8, 72076 Tübingen, Germany
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 LaTeX2e.
Results: TeXshade is the first TeX-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, TeXshade 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{at}uni-tuebingen.de
Received on July 8, 1999
; revised on September 17, 1999
; accepted on September 22, 1999
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