[Bio-software] BIRCH Bioinformatics System - Release A1.98

Brian Fristensky frist at canopus.cc.umanitoba.ca
Thu Apr 13 17:33:13 EST 2006

                    BIRCH Release A1.98

o Bluejay has been upgraded to the version dated Jan. 27, 2006
o Artemis has been upgraded to v.8
o Taverna has been upgraded to v. 1.3.1. This version fixes problems
  which caused Taverna to crash with Java 1.5.
o GDE has been upgraded to macGDE v. 2.1.5. In this version, the
  HELP button in each menu launches a standalone document viewer,
  rather than displaying the documentation in the menu itself. 
o The CopyOut and PasteIn commands for dGDE, GDE, mGDE and tGDE now
  use separate clipboard files. For example, the PastIn for tGDE will
  past in the most recent clipboard contents from tGDE, and PasteIn
  for dGDE will paste in the most recent clipboard contents from dGDE.
o Leash has been upgraded to version 2.2. This version includes
  new command line parameters, -mpil and -mpif, which make it possible
  for Leash to take lists of data as input for SeqHound methods
  which only allow a single data item (eg. SHoundSequenceLength).
  Previously, leash had to be called for each item in the list.
  A number of dGDE method calls have been updated to take advantage
  of the increased efficiency of these parameters.

o Added new features to BACHREST that gives the user more ways to narrow
  the list of enzymes and digests shown in the output. Searches can be limited
  to enzymes that generate 5' protruding, blunt or 3' protruding ends, or that
  have either symmetric or asymmetric recognition sequences. The parameters
  LEASTFRAGS and MOSTFRAGS also allow you to only print digests with at least
  LEASTFRAGS fragments, or at most MOSTFRAGS. It is also possible to
  keep the output file small by setting PRINTFRAGS. When the number of fragments
  in a digest exceeds PRINTFRAGS, MULTIDIGEST will only print the number
  of fragments, rather than printing all of the fragments themselves.
  Finally, BACHREST now prints the values of these parameters in the
  header lines of the output file.
  The maximum sequence size allowed by BACHREST has been increased to 
  20,000,000, allowing most bacterial genomes to be read. However,
  for very large sequences, BACHREST must be used at the command line. GDE
  will only read sequences that are 750K or smaller.

  To avoid conflict with the Solaris 10 digest command, DIGEST has been
  renamed as MULTIDIGEST. MULTIDIGEST has been updated to read the
  new BACHREST output file format.

Also, see what else is new with BIRCH, from the 
presentation at the Plant and Animal Genome Conference XIV:


The latest release of BIRCH (A1.98) is available at the 
BIRCH Web site


under the link 'BIRCH Administrator's Guide'.

Brian Fristensky               
Department of Plant Science      
University of Manitoba         
Winnipeg, MB R3T 2N2  CANADA   
frist at cc.umanitoba.ca 
Phone:            204-474-6085
FAX:              204-474-7528             

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