A platform-independent graphical user interface for SEQSEE and XALIGN

CABIOS APPLICATIONS NOTE Vol. 13 no 5 1997 Pages 561-562 A platform-independent graphical user interface for SEQSEE and XALIGN David S. Wishart13, Scott Fortin2, David R. Woloschuk2, Warren Wong2, Timothy Rosborough2, Gary Van Domselaar1, Jonathan Schaeffer1 and Duane Szafron2 1 Received on May 10, 1997, accepted on May 14, 1997 SEQSEE (Wishart et cil., 1994a) and XALIGN (Wishart et cil., 1994b) are two text-based, menu-driven programs developed specifically for comprehensive protein sequence analysis. Originally compiled to run on SUN and SGI workstations only, SEQSEE and XALIGN have been distributed to more than 300 laboratories around the world. Both programs have been used in a variety of applications ranging from routine sequence analysis to the identification of previously unknown sequence relationships (Upton et cil., 1992, 1993; Dulhanty and Riordan, 1994). Since releasing these programs, we have received numerous requests asking if they could be ported to additional computer platforms (Macintosh and PC) or if the text-based menus could be replaced with a more friendly graphical user interface (GUI). In response to these and other requests, we have integrated XALIGN and SEQSEE into a single-threaded package with a uniform GUI that is fully supported by SGI (Irix Version 5.0 and higher), SUN (Solaris and SunOS 4.1.3 and higher), Macintosh (Power PC OS 7.5 and higher) and PC (Windows 95) platforms. We have chosen the Smalltalk programing language to develop our graphical interface because it allows the creation of sophisticated GUIs that look and operate almost identically across all major platforms and operating systems. In many respects, Smalltalk, which was originally developed by Xerox's PARC in the late 1970s, is a more sophisticated version of the more familiar WWW language called JAVA. In particular, Smalltalk allows the facile creation of object-oriented, platform-independent GUIs. By designing the Smalltalk GUI to access the computationally intensive back-end routines through Smalltalk function calls, we were able to preserve a substantial portion of the original SEQSEE and XALIGN code (written in C). This separation between the front-end (the GUI) and the back-end has 3 To whom correspondence should be addressed E-mail • dsw@redpoll pharmacy ualberta ca © Oxford University Press allowed for a more rapid implementation of the front-end while preserving the integrity of well-tested back-end programs. In building the SEQSEE/XALIGN interface, a total of 11 separate windows or views were constructed, including: (i) a sequence editor; (ii) an alignment editor, (iii) a simple text editor, (iv) a graph viewer/editor, (v) a dotplot viewer/editor, (vi) a helical wheel viewer/editor, (vii) a structure viewer/ editor; (viii) a sequence motif viewer, (ix) a sequence statistics viewer, (x) a data browser, (xi) a file chooser. The sequence editor supports autospacing (every 10 residues), autowrapping and mouse-driven text selection along with the usual cutting, pasting, copying and segment-deletion operations. It has a text entry filter (permitting only IUPAC standard one-letter amino acid entry), a sequence 'ruler', a sequence length and position monitor, and an editable cursor position box. The sequence editor also supports a pop-up sequence reference card and a mouse-driven, colorcoded secondary structure 'painter'. A screen shot of the sequence editor is shown in Figure 1. The alignment editor integrates the functionality of XALIGN with a general multiple sequence editor. The alignment editor includes a mouse-activated sequence browser for quick data selection and loading. It also supports sequence fragment editing, autoalignment, autoconsensus calculation, color-coded secondary structure display and an editable consensus threshold box. Also included is a mouse-driven 'painter' for multi-sequence selection. One or more partial or complete sequences can be selected with this highlighter and interactively moved to the right or left via mouse-activated arrow keys, thereby permitting manual multi-sequence alignment. A screen shot of the alignment editor is shown in Figure 1. The graph, dotplot and helical wheel viewers/editors share many similarities. All three support fully scrollable displays, stepwise and regioselective (or framed) zooming and autoscaling. They also offer full annotating and editing options, including variable color and adjustable linewidth arrows, 561 Protein Engineering Network of Centres of Excellence, Faculty of Pharmacy and department of Computing Science, University of Alberta, Edmonton, AB T6G 2N8, Canada D^.Wishart et til (C) Fig. 1. (a) Screen shot of the sequence editor (as seen in UNIX); (b) screen shot of the dotplot viewer (as seen in Macintosh); (c) screen shot of the alignment editor (as seen in Windows 95). Acknowledgements The authors wish to thank Brian Sykes, Chris Upton, Robert Boyko, Leigh Willard, Charles Cruden, Alex Nip and Eowyn Cenek for their hard work in testing, rewriting and upgrading SEQSEE and XALIGN. Financial support by the Alberta Heritage Foundation for Medical Research, the Protein Engineering Network of Centres of Excellence, NSERC and the Industrial Research Assistantship Program (NRC) is gratefully acknowledged. References boxes, lines and circles. Additionally, the graph viewer supports graph axis, title and line editing, the helical wheel viewer supports user-selectable wheel and text coloring schemes, and the dotplot viewer offers simultaneous diagonal plot and text viewing. A screen shot of the dotplot viewer is shown in Figure I. The structure viewer displays predicted secondary structure by using standard, colored, three-dimensional 'helix' and 'beta-sheet' icons. It also permits selective toggling and re-ordering of up to six different kinds of structure predictions. Membrane-spanning helices are displayed separately. The sequence motif viewer supports single or multiple motif selection and viewing including PROSITE patterns, B- and T-cell epitopes, as well as phosphorylation sites. It also per- 562 Dulhanty.A.M. and Riordan J.R. (1994) A two-domain model for the R domain of the cystic fibrosis transmembrane conductance regulator based on sequence similarities. FEBS Lett., 343, 109-114. Upton.C, Mossman.K. and McFadden.G. (1992) Encoding of a homolog of the IFN-y receptor by myxoma virus. Science, 258, 1369-1373. Upton.C., Stuart.D.T. and McFadden.G. (1993) Identification of a poxvirus gene encoding a uracil DNA glycosylase. Proc. Nail. Acad. Sci. USA, 90, 4518-4522. Wishart.D.S., Boyko.R.F, Willard,L, Richards.F.M. and Sykes.B.D. (1994a) SEQSEE: a comprehensive program suite for protein sequence analysis. Comput. Applic. Biosci., 10, 121-132. Wishart,D.S., Boyko.R.F. and Sykes.B.D. (1994b) Constrained multiple sequence alignment using XALIGN. Comput. Applic. Biosci., 10, 687-688. mits toggling between a text view and a colored graphical view of selected motifs. The sequence st (...truncated)