[Cdd-commits] r755 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Fri May 23 19:31:54 2008
New Revision: 755

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added operondb (don't know whether this is really interesting, just see the note about having contacted upstream ...


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri May 23 19:31:54 2008
@@ -1526,3 +1526,32 @@
  system designed to store genome wide information. It is currently used to
  analyze data obtained via high-throughput rapid sequencing platforms such as
  the 454 and Solexa as well as tiling array data based on various platforms.
+
+Depends: operondb
+Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
+License: to be clarified
+Pkg-Description: detect and analyze conserved gene pairs
+ Comparison of complete microbial genomes reveals a large number of
+ conserved gene clusters - sets of genes that have the same order in
+ two or more different genomes. Such gene clusters often, but not
+ always represent a co-transcribed unit, or operon. A method was
+ developed to detect and analyze conserved gene pairs - pairs of genes
+ that are located close on the same DNA strand in two or more
+ bacterial genomes. For each conserved gene pair, an estimate of
+ probability is calculated that the genes belong to the same
+ operon. The algorithm takes into account several alternative
+ possibilities. One is that functionally unrelated genes may have the
+ same order due simply because they were adjacent in a common
+ ancestor. Other possibilities are that genes may be adjacent in two
+ genomes by chance alone, or due to horizontal transfer of the gene
+ pair.
+ .
+ The method is modified from the one described in: Maria D. Ermolaeva,
+ Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
+ Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
+ .
+ OperonDB was supported by the NIH under grant R01-LM007938 and by the
+ NSF under grant DBI-0234704.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
+ no info about license or downloadable code found, but tried to
+ contact authors.