From owner-comp-bio@hgmp.mrc.ac.uk Mon Apr 2 19:57:25 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AE72D17B11 for ; Mon, 2 Apr 2001 19:57:24 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2295017AF3 for ; Mon, 2 Apr 2001 19:57:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 4C52C17B1D; Mon, 2 Apr 2001 19:57:15 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4A5A417A64 for ; Mon, 2 Apr 2001 11:54:23 +0100 (BST) Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9E5D617A5E for ; Mon, 2 Apr 2001 11:54:18 +0100 (BST) Received: from mail.fu-berlin.de (mail.fu-berlin.de [160.45.11.165]) by mailbox2.ucsd.edu (8.11.0/8.11.0) with ESMTP id f32Asik29140 for ; Mon, 2 Apr 2001 03:54:44 -0700 (PDT) Received: by mail.fu-berlin.de (Smail3.2.0.98) from Curry.ZEDAT.FU-Berlin.DE (160.45.10.36) with esmtp id ; Mon, 2 Apr 2001 12:54:15 +0200 (MEST) Received: by Curry.ZEDAT.FU-Berlin.DE (Smail3.2.0.98) from news.fu-berlin.de with bsmtp id ; Mon, 2 Apr 2001 12:54:15 +0200 (MEST) To: bionet-biology-computational@moderators.isc.org From: January Weiner Newsgroups: bionet.biology.computational Subject: Arka 0.06 released Message-ID: <9a9lom$42rk1$2@fu-berlin.de> References: <99g6fb$137g7$3@fu-berlin.de> X-Orig-NNTP-Posting-Host: aixterm1.urz.uni-heidelberg.de (129.206.119.41) X-Orig-X-Trace: fu-berlin.de 986208854 4288129 129.206.119.41 (16 1086 1089 1090) X-Orig-Path: not-for-mail X-Organization: Klub Nieszkodliwych Manjakow X-KNM: http://www.knm.org.pl/ X-KF: http://www . rzuser.uni-heidelberg.de/~jweiner1/filter User-Agent: tin/pre-1.4-981002 ("Phobia") (UNIX) (AIX/4-2) Date: Mon, 2 Apr 2001 19:57:15 +0100 (BST) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk Arka is a simple graphical user interface for command line programs, with the focus on the gp package of sequence analysis tools (http://www.bioinformatics.org/genpak). The program reads a description of the command line tools from a text file and produces a GUI dialog upon users request. Then, the command line program is executed, and output / error messages can be recorded and edited. Together with the gp programs, it features: * simple sequence searches * promoter searches [*] * codon usage analysis * ORF searches and converting DNA sequences to protein sequences * pattern frequency analyses * converting DNA sequences to cross-correlated variable matrices * Tm primer analysis * analysis of primer secondary structures and dimeres * simple restriction site analysis * on-the-fly creation of PNG graphical gene maps Changes in 0.06 include several bugfixes, full GUI editing and creation of the specifications of the command line programs (you can, for example, create easily a dialog for the blasta program family), and better job control. Arka is written in C/ Gtk+, so it is mainly for Unix systems. It is quick, small, does not depend on GNOME/KDE and is early beta :-). In theory, it could serve as a GUI for any command line programs, from blasta to zip, it is just a matter of creating a specification file. Apart from being a user interface for other programs, there are two small visualisation tools -- one for creating *very* primitive GC contents graphs and one for fully interactive displaying 3D graphs (which I coded to visualize some DNA structural features I was working on). You'll find it on http://www.bioinformatics.org/genpak/. I am interested in any comments on the programs usability. An example of using the gp programs in CGI scripts can be found on http://www.zmbh.uni-heidelberg.de/M_pneumoniae/Matrix . Best regards, January [*] using the Hertz matrix method, for details see Weiner, J., R. Herrmann and G.F. Browning 2000, Nucleic Acids Res. 28:4488-96. -- ----)-\//-///-----------------------------------January-Weiner-3------- The art of flying is to throw yourself at the ground and miss. .