GeneWeb II: Sequence Analysis Tools on Web ServerUsing Java API

Ken Kurokawa 1

ken@gen-info.osaka-u.ac.jp

Tatsuya Takagi 3

Kenichi Kawashima 2
kawasima@senri-i.or.jp

ttakagi@phs.osaka-u.ac.jp
123

Toshiyuki Okumura 2
okumura@senri-i.or.jp

Teruo Yasunaga 1

yasunaga@gen-info.osaka-u.ac.jp

Genome Information Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
Senri International Information Institute, Senri Life Science Center, 1-4-2, SinsenriHigashimachi, Toyonaka, Osaka 565-0082, Japan.
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita,
Osaka 565-0871, Japan.

1 Introduction
In recent years, the computer network, including Internet, came into wide use and researchers inmany elds came to utilize it routinely. World Wide Web (WWW) and its browser software such as
Netscape or Internet Explorer are probably the most powerful and useful tools for researchers whosearch documents or retrieve information from remote computers distributed over Internet. Especiallyin molecular and genome biology, researchers need to access to the various extremely large biological
database on the network and to retrieve them. Therefore, the researchers are expected to be accustomed to use Web browser, even if they are not familiar with the computer operation other thanWeb browser. In this aspect, we had been developing sequence analysis tools on Web server named
GeneWeb I in 1995 [1]. This system provided sequence analysis tools which was available on Web
browser in any kind of computers.
For improving graphical user interface (GUI), we have been developing new software named GeneWeb II (Fig. 1) which is developed by using Java Application Programming Interface (Java API)for GUI and for interfacing external applications with Web server.

2 GeneWeb II
GeneWeb II programmed by Java API was compiled to architecture neutral byte code format.
So, it can be executed on many di erent kinds of computers such as a IBM PC, a Macintosh andetc. with `Java Virtual Machine'. GeneWeb II supports various analysis tools, most of which areestablished free software such as fasta, blast, clustalw and so on, for a single and multiple nucleotide
or amino acid sequences; including format conversion, sequence data acquisition from databases,nucleotide or amino acids contents, restriction enzyme map, codon usage, translation, open reading
frame, homology searches, multiple sequence alignment, phylogenetic tree reconstruction and so on.
In addition, GeneWebII is designed for that it is feasible to update the tools and import new sequence
analysis tools in GeneWeb II. Furthermore, the gure of the result for, for example, phylogenetic treeor the secondary structure of sequence, is also provided in PostScript le with high quality suitablefor publication.
There are several advantages of GeneWeb II compared with GeneWeb I which used Common
Gateway Interface (CGI) as the interface between Web server and applications. First of all, using236

Figure 1: Examples of sequence analyses on GeneWeb II.
Application Windowing Toolkit (java.awt), the user interface is improved by its excellent GUI components. Because the processes, such as checking input parameter, displaying arrows , and etc., areexecuted on the client computers, the load of server computer is reduced. Moreover, the load of thenetwork communication is also reduced in GeneWeb II.
However, as Java system is also still under development, it has some bugs. There is no guarantee
about the workings of the application on every platform. Indeed, in a Macintosh, GeneWeb II can not
be executed on even the latest version of Netscape Communicator (version 4.5b2). We expect that
this problem will be resolved in near future.
GeneWeb II is accessible from the WWW page of our center(http://www.gen-info.osaka-u.ac.jp/),and the on-line manual are also available on our WWW page in Portable Document Format (PDF)
le. To use GeneWeb II, user is requested to enter user name and password. A guest user is also
welcome to use it with entering the e-mail address as password, although some functions such as batchprocessing and history function are unavailable.

References[1] Yasunaga, T., Takagi, T., Takeuchi, A. and Niiyama, T., Developing Sequence Analysis Tools
on Web Server, Proc. Genome Informatics Workshop 1995, Universal Academy Press, 164{165,1995.

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