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  • News & Commentary - Message forums

    BIRCH A1.98 - updates and new features
    Submitted by Brian Fristensky; posted on Monday, April 17, 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'.

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