Add dotter 20021204 # last modified date in FTP server, a viewer for

multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>

4 files changed, 63 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index f8ecae099be7..1cac172ec073 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -18,6 +18,7 @@
     SUBDIR += crimap
     SUBDIR += distribfold
     SUBDIR += dna-qc
+    SUBDIR += dotter
     SUBDIR += embassy
     SUBDIR += emboss
     SUBDIR += fasta
diff --git a/biology/dotter/Makefile b/biology/dotter/Makefile
new file mode 100644
index 000000000000..239a4c5811a9
--- /dev/null
+++ b/biology/dotter/Makefile
@@ -0,0 +1,40 @@
+# ex:ts=8
+# New ports collection makefile for:	dotter
+# Date created:				11 Jan 2006
+# Whom:					Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	dotter
+PORTVERSION=	20021204 # last modified date in FTP server
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.cgb.ki.se/pub/esr/dotter/
+DISTNAME=	${PORTNAME}.LIN
+EXTRACT_SUFX=	#
+DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
+EXTRACT_ONLY=	#
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	A viewer for multiple sequence alignments
+
+USE_LINUX=	yes
+
+NO_BUILD=	yes
+PLIST_FILES=	bin/${PORTNAME} bin/${DISTNAME}
+
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} != "i386"
+IGNORE=		there are also executables for Alpha and Sparc \
+		but they are for OSF and Solaris ... do they  \
+		run on FreeBSD-Sparc and FreeBSD-alpha?
+.endif
+
+do-install:
+	${BRANDELF} -t Linux ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}
+	${INSTALL_PROGRAM} ${DISTDIR}/${DIST_SUBDIR}/${DISTNAME} \
+	${PREFIX}/bin
+	( cd ${PREFIX}/bin && ${LN} -s ${DISTNAME} ${PORTNAME} )
+
+.include <bsd.port.post.mk>
diff --git a/biology/dotter/distinfo b/biology/dotter/distinfo
new file mode 100644
index 000000000000..a4a8cd00d4e7
--- /dev/null
+++ b/biology/dotter/distinfo
@@ -0,0 +1,3 @@
+MD5 (dotter-20021204/dotter.LIN) = a308eb0b710b5e3e741ee09bd4b0982e
+SHA256 (dotter-20021204/dotter.LIN) = c66bae7704b2fa305f848451cf35b7a0738a3fd57468da1393684328f111cd75
+SIZE (dotter-20021204/dotter.LIN) = 4804333
diff --git a/biology/dotter/pkg-descr b/biology/dotter/pkg-descr
new file mode 100644
index 000000000000..1f04ae8b9118
--- /dev/null
+++ b/biology/dotter/pkg-descr
@@ -0,0 +1,19 @@
+Dotter is a graphical dotplot program for detailed comparison of two sequences.
+Here, every residue in one sequence is compared to every residue in the other
+sequence. The first sequence runs along the x-axis and the second sequence
+along the y-axis. In regions where the two sequences are similar to each other,
+a row of high scores will run diagonally across the dot matrix. If you're
+comparing a sequence against itself to find internal repeats, you'll notice
+that the main diagonal scores maximally, since it's the 100% perfect
+self-match.
+
+To make the score matrix more intelligible, the pairwise scores are averaged
+over a sliding window which runs diagonally. The averaged score matrix forms a
+three-dimensional landscape, with the two sequences in two dimensions and the
+height of the peaks in the third. This landscape is projected onto two
+dimensions by aid of greyscales - the darker grey of a peak, the higher it is.
+
+Dotter provides a tool to explore the visual appearance of this landscape, as
+well as a tool to examine the sequence alignment it represents.
+
+WWW: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html