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Msatfinder - Message forums
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Welcome to Open Discussion
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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.
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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.
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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.
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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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