[Blends-commit] r2486 - in /projects/med/trunk/debian-med/tasks: bio imaging imaging-dev

Tue Nov 23 16:52:26 UTC 2010

Author: tille
Date: Tue Nov 23 16:52:13 2010
New Revision: 2486

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2486
Log:
Added pal2nal

Modified:
    projects/med/trunk/debian-med/tasks/bio
    projects/med/trunk/debian-med/tasks/imaging
    projects/med/trunk/debian-med/tasks/imaging-dev

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2486&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Tue Nov 23 16:52:13 2010
@@ -3317,6 +3317,28 @@
  Maqview is based on OpenGL. Installing OpenGL on your system is the                                       trade-off of getting a better feel and look. The following screenshots
  show the two viewing modes of Maqview.
 
+Depends: pal2nal
+WNPP: 604701
+Responsible: Steffen Moeller <moeller at debian.org>
+Homepage: http://www.bork.embl.de/pal2nal/
+License: to be clarified
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pal2nal/trunk/
+Pkg-Description: converts proteins to genomic DNA alignment
+ PAL2NAL is a program that converts a multiple sequence alignment
+ of proteins and the corresponding DNA (or mRNA) sequences into
+ a codon-based DNA alignment. The program automatically assigns
+ the corresponding codon sequence even if the input DNA sequence
+ has mismatches with the input protein sequence, or contains UTRs,
+ polyA tails. It can also deal with frame shifts in the input
+ alignment, which is suitable for the analysis of pseudogenes.
+ The resulting codon-based DNA alignment can further be subjected
+ to the calculation of synonymous (Ks) and non-synonymous (Ka)
+ substitution rates.
+Published-Title: PAL2NAL: robust conversion of protein sequence alignment into the corresponding codon alignments.
+Published-Authors: Mikita Suyama, David Torrents, and Peer Bork
+Published-In: Nucleic Acids Res. 34:W609-W612
+Published-Year: 2006
+
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html

Modified: projects/med/trunk/debian-med/tasks/imaging
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/imaging?rev=2486&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging (original)
+++ projects/med/trunk/debian-med/tasks/imaging Tue Nov 23 16:52:13 2010
@@ -695,16 +695,6 @@
 
 
 Depends: mriconvert
-Homepage: http://lcni.uoregon.edu/~jolinda/MRIConvert/
-License: GPL
-Responsible: Steve M. Robbins <smr at debian.org>
-WNPP: 599880
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mriconvert/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mriconvert/trunk/
-Pkg-Description: converts DICOM files to other formats
- MRIConvert is a medical image file conversion utility that converts
- DICOM files to NIfTI 1.1, Analyze 7.5 , SPM99/Analyze, BrainVoyager,
- and MetaImage volume formats.
 
 
 Depends: connectomeviewer

Modified: projects/med/trunk/debian-med/tasks/imaging-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/imaging-dev?rev=2486&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging-dev (original)
+++ projects/med/trunk/debian-med/tasks/imaging-dev Tue Nov 23 16:52:13 2010
@@ -142,24 +142,7 @@
 Published-In: Preprint
 Published-URL: http://hal.archives-ouvertes.fr/inria-00467061/en/
 
-
 Depends: python-nibabel
-License: Expat
-WNPP: 600275
-Responsible: NeuroDebian Team <team at neuro.debian.net>
-Homepage: http://nipy.sourceforge.net/nibabel
-Pkg-URL: http://neuro.debian.net/pkgs/python-nibabel.html
-Vcs-Git: git://git.debian.org/git/pkg-exppsy/pynifti.git
-Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/pynifti.git
-Pkg-Description: Python bindings to various neuroimaging data formats
- This package provides read and write access to some common medical and
- neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
- NIfTI1, MINC, as well as PAR/REC. The various image format classes give full
- or selective access to header (meta) information and access to the image data
- is made available via NumPy arrays.  NiBabel is the successor of PyNIfTI.
- .
- This package also provides a commandline tool for conversion of PAR/REC to
- NIfTI images.
 
  ; Added by blends-inject 0.0.2. [Please note here if modified manually]
 Depends: libgdf-dev


