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  • Msatfinder - Message forums

    Discussion forums: Open Discussion

    Expanded view | Monitor forum | Save place

    Welcome to Open Discussion
    Submitted by Unset; posted on Thursday, February 17, 2005
    Welcome to Open Discussion
    New version
    Submitted by Milo Thurston; posted on Monday, March 21, 2005
    The 1.6.7 version has recently been released. This fixes a bug in one of the search engines (causing it to slow down on large sequences) and adds spinners to pass the time whilst performing some slow Bioperl operations.
    Interrupted repeats
    Submitted by Milo Thurston; posted on Thursday, July 07, 2005
    A script to look through the results in order to find interrupted microsatellites is now available: http://www.bioinf.ceh.ac.uk/msatfinder/ird.html (also in CVS on bioinformatics.org). We intend to incorporate this functionality into msatfinder shortly, but meanwhile any comments on the utility of this code would be appreciated.
    New Version
    Submitted by Milo Thurston; posted on Monday, July 11, 2005
    We've just put up a version 2.0 that includes the code for finding interrupted microsatellites, plus an additional summary file for all primers found.
    Perl regex bug
    Submitted by Milo Thurston; posted on Thursday, August 18, 2005
    It has come to light that on rare occasions some data may fall foul of a bug in Perl's regex engine that causes a segmentation fault. The perl developers say: <blockquote> This ticket is for bugs related to the overflow of the OS stack during recursion in the perl regex engine. Generally they can be "worked around" by increasing the stack size by using ulimit (bash/sh/ksh/zsh) or limit (csh/tcsh). The long term plan is to rewrite the regex engine to not use the stack for recursion. </blockquote> Changing the stack size has not proven effective on the on-line version, but we are upgrading to a development version of Perl upon which the problem is less severe. The -e3 setting on the command line version of msatfinder works around the problem, but is slow.
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