[Blends-commit] r1859 - projects/med/trunk/debian-med/tasks

[Debian Pure Blends Subversion Commit]

Author: moeller
Date: Fri Aug 28 16:38:09 2009
New Revision: 1859
URL: http://svn.debian.org/viewsvn/blends?rev=1859&view=rev

Log:
Added more references.


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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1859&view=diff&r1=1859&r2=1858&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri Aug 28 16:38:09 2009
@@ -23,7 +23,43 @@
 
 X-Begin-Category: Sequence alignments and related programs.
 
-Depends:     amap-align, blast2, boxshade, gff2aplot, kalign, mafft, mummer, muscle, sim4, sibsim4, t-coffee, wise
+Depends:     amap-align, boxshade, gff2aplot, muscle, sim4, sibsim4, wise
+
+Depends: mummer
+Published-Title: Versatile and open software for comparing large genomes
+Published-Authors: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, S.L. Salzberg
+Published-In: Genome Biol. 5(2):R12
+Published-Year: 2004
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14759262
+
+Depends: blast2
+Published-Title: Basic local alignment search tool
+Published-Authors: S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman
+Published-In: J Mol Biol. 215(3):403-410
+Published-Year: 1990
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/2231712
+
+Depends: mafft
+Published-Title: Multiple alignment of DNA sequences with MAFFT
+Published-Authors: K. Katoh, G. Asimenos, H. Toh
+Published-In: Methods Mol Biol. 537:39-64
+Published-Year: 2009
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19378139
+
+
+Depends: t-coffee
+Published-Title: T-Coffee: A novel method for multiple sequence alignments
+Published-Authors: C. Notredame, D. Higgins, J. Heringa
+Published-In: Journal of Molecular Biology 302(1):205-217
+Published-Year: 2000
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
+
+Depends: kalign
+Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
+Published-Authors: Lassmann T, Sonnhammer EL.
+Published-In: BMC Bioinformatics, 6:298
+Published-Year: 2005
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16343337
 
 Depends: hmmer
 Published-Title: Multiple Alignment Using Hidden Markov Models.
@@ -35,7 +71,7 @@
 Depends: exonerate
 Published-Title: Automated generation of heuristics for biological sequence comparison
 Published-Authors: G.C. Slater, E. Birney
-Published-In: BMC Bioinformatics, 6:31
+Published-In: BMC Bioinformatics 6:31
 Published-Year: 2005
 Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
 X-Published-doi: doi:10.1186/1471-2105-6-31
@@ -52,11 +88,12 @@
 Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
 Published-In: Algorithms for Molecular Biology 3:6
 Published-Year: 2008
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
 
 Depends: poa
-Published-Authors: Christopher Lee
-X-Comment: I hope the Copyright owner is the Author of the publication.  Please FIX it if I'm wrong!!!
-Published-In: Bioinformatics 10;20(10):1546-1556. 
+Published-Authors: C. Grasso, C. Lee
+Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
+Published-In: Bioinformatics 20(10):1546-1556. 
 Published-Year: 2004
 
 Depends: probcons