[Cdd-commits] r997 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Jul 22 11:36:03 2008
New Revision: 997

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added cdna_db


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Jul 22 11:36:03 2008
@@ -1747,3 +1747,41 @@
  same software is now used for many different genomic databases from
  bacteria to fungi to plants to man. It is also increasingly used for
  databases with non-biological content.
+
+Comment: If you stumble upon alfresco at
+ http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
+ tarball vanished from the downlowad page.  So this is not for us even
+ if it is linked from Sanger Institute web site.
+
+Comment: If you stumble upon angler at
+ http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because
+ it is not updated since 1997.  I found no license statement and so
+ this is probably also not for us except somebody has real interest
+ and volunteers to clarify the license.
+
+Depends: cdna_db
+Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
+License: Artistic
+Pkg-Description: quality-control checking of finished cDNA clone sequences
+ cdna_db is a software system designed for quality-control checking of
+ finished cDNA clone sequences, and their computational analysis. The
+ combination of a relational db (MySQL) schema, and an
+ object-orientated perl API make it easy to implement high-level
+ analyses of these transcript sequences.
+ .
+ The cdna_db can store cDNA clone sequences, and ESTs and
+ consensus/contig sequences also derived from these clones. These are
+ then used by the system to check cDNA clone sequence identity etc
+ (see deneral_doc.txt). For each clone multiple DNA sequence versions
+ can be stored, if for instance, the finished DNA sequence is revised
+ as part of the sequencing process.
+ .
+ A blast pipeline is implemented together with a job control system
+ (with LSF underlying) so that multiple CPUs can be used in parallel
+ to carry out the blasts of large datasets. The searches can be made
+ incremental, so as more cDNA sequences are added to the databank,
+ just the new clones are blasted.
+ .
+ Utility scripts are provided to delete previous search results, and
+ dump cDNA clones sequences (such as those that passed the QC
+ checking) from the cdna_db.