From owner-comp-bio@hgmp.mrc.ac.uk Tue May 8 00:05:53 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6266A17B03 for ; Tue, 8 May 2001 00:05:52 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0254617B04 for ; Tue, 8 May 2001 00:05:49 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id A2F6B17B03; Tue, 8 May 2001 00:05:45 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4B48617ADD for ; Thu, 3 May 2001 10:51:38 +0100 (BST) Received: from mailbox4.ucsd.edu (mailbox4.ucsd.edu [132.239.1.56]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9843917ACB for ; Thu, 3 May 2001 10:51:32 +0100 (BST) Received: from mail.fu-berlin.de (mail.fu-berlin.de [160.45.11.165]) by mailbox4.ucsd.edu (8.10.1/8.11.0) with ESMTP id f439pVg14361 for ; Thu, 3 May 2001 02:51:31 -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 ; Thu, 3 May 2001 11:51:30 +0200 (MEST) Received: by Curry.ZEDAT.FU-Berlin.DE (Smail3.2.0.98) from news.fu-berlin.de with bsmtp id ; Thu, 3 May 2001 11:51:29 +0200 (MEST) To: bionet-biology-computational@moderators.isc.org From: January Weiner Newsgroups: bionet.biology.computational Subject: Arka 0.08 released Message-ID: <9cr9n0$f88qo$1@fu-berlin.de> References: <99g6fb$137g7$3@fu-berlin.de> <9a9lom$42rk1$2@fu-berlin.de> X-Orig-NNTP-Posting-Host: aixterm1.urz.uni-heidelberg.de (129.206.119.41) X-Orig-X-Trace: fu-berlin.de 988883488 15999832 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: Tue, 8 May 2001 00:05:45 +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: * sequence editor * simple sequence searches * interface for various unix utilities (find, grep et co.) * 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 Changes in 0.08 include reworked GP and unix program specifications, minor bugfixes and configurable shortcuts for menu items. Changes in 0.07 include many major bugfixes and a new utility -- a sequence editor. 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) and a sequece editor tool. 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------- A machine is only a machine because it cannot think - G.K.Chesterton .