E Beitz1. 1. Faculty of Chemistry and Pharmacy, University of Tübingen, Germany. eric.beitz@uni-tuebingen.de
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 LATEX2 epsilon. 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.h tml (macro package and on-line documentation) CONTACT: eric.beitz@uni-tuebingen.de
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 LATEX2 epsilon. 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.h tml (macro package and on-line documentation) CONTACT: eric.beitz@uni-tuebingen.de
Authors: Margaret A Holmes; Frederick S Buckner; Wesley C Van Voorhis; Christopher Mehlin; Erica Boni; Thomas N Earnest; George DeTitta; Joseph Luft; Angela Lauricella; Lori Anderson; Oleksandr Kalyuzhniy; Frank Zucker; Lori W Schoenfeld; Wim G J Hol; Ethan A Merritt Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun Date: 2006-02-24
Authors: Tracy Arakaki; Isolde Le Trong; Eric Phizicky; Erin Quartley; George DeTitta; Joseph Luft; Angela Lauricella; Lori Anderson; Oleksandr Kalyuzhniy; Elizabeth Worthey; Peter J Myler; David Kim; David Baker; Wim G J Hol; Ethan A Merritt Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun Date: 2006-02-24