Test Platform

SeqWeb was maintained on a Silicon Graphics Origin 200 server with 2-180MHz CPUs and 256 Mb RAM. SeqWeb was accessed using Netscape Communicator 4.03, or Internet Explorer 4.0 running on a Pentium 166MHz system with 80 Mb RAM, via Ethernet and 28.8 modem connections.

Introduction

SeqWeb is Genetic Computer Group's Web-based graphical interface to the GCG Wisconsin Package, a comprehensive suite of sequence analysis software for DNA and proteins. SeqWeb provides easy access to core programs in the GCG Wisconsin Package through a Web browser-based graphical interface, eliminating the need to memorize command-line syntax. SeqWeb offers a list of options for each program, with default values already selected, making it easy for novice users to utilize quickly GCG's basic features.

Unfortunately, this added convenience is accompanied by several limitations. Users will find that certain functions available in GCG are not accessible with SeqWeb. In addition, the available programs offer fewer options than are available from the command line. Some of the programs accessible with SeqWeb include tools for sequence comparison, multiple sequence alignment, database searching, pattern recognition, and gene finding, as well as primer selection, protein analysis, translation, and RNA secondary structure. Notably missing from SeqWeb are fragment assembly features, the multiple alignment editor available in SeqLab (the free graphical user interface included with GCG), and batch processing of analysis tasks. The occasional user of GCG will appreciate SeqWeb's features, but advanced users of the command-line interface may find the limitations frustrating.

SeqWeb is sold as a separate site license, and requires users to purchase a license for GCG Wisconsin Package 9.1. It runs on Digital Unix, IRIX, and Solaris platforms, and is designed to run locally on a site along with GCG Wisconsin Package, although they can be maintained on separate computers. Password protected log-in ensures secure access to both SeqWeb and GCG. Unlike SeqLab, which is included with GCG 9.1, SeqWeb does not require X Window or an X Window emulator. Users log in to SeqWeb via Web browsers such as Netscape Navigator or Internet Explorer 4.0 (or later), making access to GCG truly platform independent.

Javascript is used extensively in SeqWeb. For this reason, browser properties also seem to affect the way SeqWeb performs. A few Javascript bugs appeared when SeqWeb was accessed with Netscape Navigator 4.03, though they were not evident with Internet Explorer 4.0. These bugs aside, SeqWeb provides users with an intuitive, consistent interface for initiating an analysis in GCG. Results are displayed in HTML format, with links to other resources in the Wisconsin Package as well as on the Web. For example, figure 2 shows information on the input sequence used in a gap alignment. Clicking on the View Sequence button displays the complete GenBank data file."

About this Review

This review is not an evaluation of GCG, but rather of SeqWeb, the interface to GCG. Though a variety of tasks will be presented as a part of this review, it is meant to demonstrate the features of SeqWeb rather than present a comprehensive overview of the features of GCG. In addition to SeqWeb, Genetics Computer Group offers a command-line interface to GCG, as well as SeqLab, an alternative graphical interface to GCG. SeqLab is included with the GCG 9.1 site license and does not require an additional purchase. SeqLab requires X Window, or an X Window emulator on Macintosh or Windows platforms. For this review, the author used a demo version of X-Win32 4.1 for Windows 95 to compare the features of SeqWeb with SeqLab. Contact StarNet Communications or visit their Web page for more information on X-Win32.

Program Features

SeqWeb provides access to the most commonly used programs in the Wisconsin Package, making it easy for users to retrieve and analyze DNA and protein sequences. The tools that are accessible with SeqWeb fall under eight categories: sequence comparison, multiple sequence alignment, database searching, primer selection, protein analysis, pattern recognition and gene finding, translation, and RNA secondary structure. Table 1 lists all of the programs available in GCG Wisconsin Package, as well as those accessible with SeqWeb. Although it appears that SeqWeb eliminates access to many of the features of GCG, this is not necessarily the case. For example, the program Seqed cannot be launched from SeqWeb, but a new Sequence Manager (figure 4) enables one to edit, view, and import new sequences from text files or database searches. In addition, many of the utilities and import/export conversion programs are no longer essential for effectively utilizing GCG through the Web browser interface. Unfortunately, the multiple sequence alignment editor in SeqLab (figure 5) is not available through SeqWeb, and the program completely omits fragment assembly functions.

The Sequence Manager (figure 4) allows one to load and manage sequences in SeqWeb. Users may copy, view, delete, rename, and edit sequence files. One may also add new files for analysis from a locally stored file, from the clipboard, or after a database search. Unfortunately, a Javascript bug plagued the Sequence Manager when a window was resized in Netscape Navigator. The only solution was to maximize the Navigator window, then reload the Sequence Manager page. Interestingly, this bug was not evident when accessing SeqWeb with Internet Explorer.

A variety of sequence file formats are directly compatible with SeqWeb, including FASTA, GenBank, NCBI Report Format, EMBL, IntelliGenetics, Staden, PIR, and SWISS-PROT. SeqWeb also utilizes multiple sequence format files such as GCG's RSF and MSF files. The display seen in figure 6 is displayed when BestFit, the program to align two ucleic acid sequences, is launched. After selecting the files, one simply licks on the Run button to initiate the analysis. Users can opt for the default parameter values set by SeqWeb, or scroll down the page to make changes in these values. Figure 7 shows the result of running Gap, a program that globally aligns two protein sequences.

Restriction enzyme analysis of nucleic sequences is one of the most commonly used features of any DNA analysis software package. Map is a program that enables one to display restriction maps of nucleic acid sequences or cleavage maps of peptide sequences. Users have control over a number of parameters when running Map (figure 8). For example, when doing a restriction map of a DNA sequence, one can select enzymes that cut only once, that create blunt ends, or produce 5' or 3' overhangs. One can treat sequences as linear or circular, and organize the table of results by cut position and enzyme name. Several options for displaying translation frames are available, including Three Forward Translation Frames, All Six Translation Frames, and Open Translation Frames.

Other Graphical Interfaces

SeqWeb is not the only graphical interface one can use to access GCG Wisconsin Package. Version 9.1 includes SeqLab, the graphical user interface that requires an X-Window-compatible display (or X Window emulation). SeqLab provides users with access to virtually all GCG features and optional parameters, and includes an impressive color-coded multiple sequence editor (figure 5).

Marc Colet of the Department of Molecular Biology at the Free University of Brussels has developed WWW2GCG (figure 9), an effective Web-browser based interface to GCG Wisconsin Package that is available as a free download. Users can access a demo of this interface with the user name &qupt;w2g_demo" and password "WWW2gcg!" (without the quotes). Note that this demo only enables one to see the interface, and does not actually link to any of the GCG programs.

WWW2GCG is a set of programs and scripts that facilitates access to the GCG software programs by providing users with an intuitive interface. Version 5.0 of WWW2GCG is based on the SeqLab configuration files, and includes all of the SeqLab rules set up at one's site. It was developed using Perl, and can be run on Digital Unix and on Solaris. It has also been tested with both Apache and NCSA Web servers. Users can obtain WWW2GCG as a small C program that must be compiled on one's local machine. One can retrieve it by anonymous FTP.

SeqWeb is a Web-browser-based graphical interface for GCG Wisconsin Package that will satisfy most novice users, but may frustrate those accustomed to the command-line. As an initial attempt, SeqWeb does a fine job of making most of the core programs in GCG easily accessible, although some of the minor Javascript bugs indicate it may not yet be ready for general use in the research community. At a price tag of $2,500, it may be prohibitively expensive for many research sites. For those institutions with many novice users, it may be more economical to offer an easy-to-use graphical interface such as SeqWeb, rather than provide extensive resources for support. Although it requires an X-Window-compatible display, SeqLab integrates more features and options, and may enable end users to wait until GCG releases SeqWeb 1.1 with Wisconsin Package 10.0.

SeqWeb requires GCG Wisconsin Package 9.1, and will run on Digital Unix, IRIX, and Solaris platforms. Contact Genetics Computer Group by email for more information, as well as for time-limited access to SeqWeb for user evaluation. Version 1.1 of SeqWeb will be released with GCG Wisconsin Package 10.0 later this year. Additional programs and batch processing support are some of the enhancements expected.

SeqWeb 1.0 is available for $2,500 (academic price) from Genetics Computer Group. For a price quote, have your Wisconsin Package site manager contact GCG at seqweb@gcg.com. Genetics Computer Group can be contacted by mail at 575 Science Drive, Madison, Wisconsin 53711, by phone at (608) 231-5200, by fax at (608) 231-5202, or by email. Visit the GCG Web site to learn more about SeqWeb or about their other analysis products.