Subject: CVS commit: pkgsrc/biology/align
To: None <>
From: Jan Schaumann <>
List: pkgsrc-changes
Date: 09/26/2003 03:10:20
Module Name:	pkgsrc
Committed By:	jschauma
Date:		Fri Sep 26 03:10:20 UTC 2003

Update of /cvsroot/pkgsrc/biology/align
In directory

Log Message:
Initial import of pdbalign-20030812, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

Given a GCG multiple sequence alignment file (a GCG MSF file), which a 
includes a sequence of known structure, the program pdbalign maps the 
sequence variability onto the known structure. The central premise is 
of course, that for a closely related family of proteins (sequence ID 
> 40%) the 3-D structures will not be significantly different.pdbdist 
calculates the distance from each atom in the pdb file to each atom in 
the ligand and records the minimum in the temperature field for that 
atom record.distalign reads the output from pdbdist and also the 
original GCG MSF file and produces an MSF file annotated with a 
measure of sequence variability and the distance of the residue at 
that position (of the sequence of known structure) from the ligand. 

Vendor Tag:	TNF
Release Tags:	pkgsrc-base
N pkgsrc/biology/align/Makefile
N pkgsrc/biology/align/DESCR
N pkgsrc/biology/align/PLIST
N pkgsrc/biology/align/distinfo
N pkgsrc/biology/align/patches/patch-aa
N pkgsrc/biology/align/patches/patch-ab
N pkgsrc/biology/align/patches/patch-ac
N pkgsrc/biology/align/patches/patch-ad

No conflicts created by this import