From owner-freebsd-ports-bugs@FreeBSD.ORG Wed Feb 8 19:20:08 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id D894916A420 for ; Wed, 8 Feb 2006 19:20:08 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 04B2C43D49 for ; Wed, 8 Feb 2006 19:20:06 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k18JK61q010448 for ; Wed, 8 Feb 2006 19:20:06 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k18JK6mV010447; Wed, 8 Feb 2006 19:20:06 GMT (envelope-from gnats) Resent-Date: Wed, 8 Feb 2006 19:20:06 GMT Resent-Message-Id: <200602081920.k18JK6mV010447@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Fernan Aguero Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id E594816A420 for ; Wed, 8 Feb 2006 19:15:06 +0000 (GMT) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (omega.iib.unsam.edu.ar [170.210.49.14]) by mx1.FreeBSD.org (Postfix) with ESMTP id AFE8643D53 for ; Wed, 8 Feb 2006 19:15:05 +0000 (GMT) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (localhost [127.0.0.1]) by omega.iib.unsam.edu.ar (8.13.4/8.13.4) with ESMTP id k18JF3jv041000 for ; Wed, 8 Feb 2006 16:15:03 -0300 (ART) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: (from fernan@localhost) by omega.iib.unsam.edu.ar (8.13.4/8.13.3/Submit) id k18JF3YN040999; Wed, 8 Feb 2006 16:15:03 -0300 (ART) (envelope-from fernan) Message-Id: <200602081915.k18JF3YN040999@omega.iib.unsam.edu.ar> Date: Wed, 8 Feb 2006 16:15:03 -0300 (ART) From: Fernan Aguero To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/93055: [ new port ] biology/dotter X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 08 Feb 2006 19:20:09 -0000 >Number: 93055 >Category: ports >Synopsis: [ new port ] biology/dotter >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Feb 08 19:20:06 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: See COMMENT and pkg-descr >How-To-Repeat: >Fix: --- dotter.shar begins here --- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # dotter # dotter/Makefile # dotter/distinfo # dotter/pkg-descr # echo c - dotter mkdir -p dotter > /dev/null 2>&1 echo x - dotter/Makefile sed 's/^X//' >dotter/Makefile << 'END-of-dotter/Makefile' X# ex:ts=8 X# New ports collection makefile for: dotter X# Date created: 11 Jan 2006 X# Whom: Fernan Aguero X# X# $FreeBSD$ X# X XPORTNAME= dotter XPORTVERSION= 20021204 # last modified date in FTP server XCATEGORIES= biology XMASTER_SITES= ftp://ftp.cgb.ki.se/pub/esr/dotter/ XEXTRACT_SUFX= # XEXTRACT_ONLY= # XDIST_SUBDIR= ${PORTNAME}-${PORTVERSION} X XMAINTAINER= fernan@iib.unsam.edu.ar XCOMMENT= A viewer for multiple sequence alignments X X.include X X.if ${ARCH} == "i386" XDISTNAME= ${PORTNAME}.LIN XUSE_LINUX= yes X.else XIGNORE= There are also executables for Alpha and Sparc \ X but they are for OSF and Solaris ... do they \ X run on FreeBSD-Sparc and FreeBSD-alpha? X.endif X XNO_BUILD= yes XPLIST_FILES= bin/${PORTNAME} bin/${DISTNAME} X Xdo-install: X ${BRANDELF} -t Linux ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} X ${INSTALL_PROGRAM} ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} \ X ${PREFIX}/bin X ( cd ${PREFIX}/bin && ${LN} -s ${DISTNAME} ${PORTNAME} ) X X.include END-of-dotter/Makefile echo x - dotter/distinfo sed 's/^X//' >dotter/distinfo << 'END-of-dotter/distinfo' XMD5 (dotter-20021204/dotter.LIN) = a308eb0b710b5e3e741ee09bd4b0982e XSHA256 (dotter-20021204/dotter.LIN) = c66bae7704b2fa305f848451cf35b7a0738a3fd57468da1393684328f111cd75 XSIZE (dotter-20021204/dotter.LIN) = 4804333 END-of-dotter/distinfo echo x - dotter/pkg-descr sed 's/^X//' >dotter/pkg-descr << 'END-of-dotter/pkg-descr' XDotter is a graphical dotplot program for detailed comparison of two sequences. XHere, every residue in one sequence is compared to every residue in the other Xsequence. The first sequence runs along the x-axis and the second sequence Xalong the y-axis. In regions where the two sequences are similar to each other, Xa row of high scores will run diagonally across the dot matrix. If you're Xcomparing a sequence against itself to find internal repeats, you'll notice Xthat the main diagonal scores maximally, since it's the 100% perfect Xself-match. X XTo make the score matrix more intelligible, the pairwise scores are averaged Xover a sliding window which runs diagonally. The averaged score matrix forms a Xthree-dimensional landscape, with the two sequences in two dimensions and the Xheight of the peaks in the third. This landscape is projected onto two Xdimensions by aid of greyscales - the darker grey of a peak, the higher it is. X XDotter provides a tool to explore the visual appearance of this landscape, as Xwell as a tool to examine the sequence alignment it represents. X XWWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html END-of-dotter/pkg-descr exit --- dotter.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted: