GCG 9.0 FASTA and EPD - core dump! GCG reply

Aengus Stewart aengus.stewart at icrf.icnet.uk
Wed Sep 24 09:04:11 EST 1997

I got this reply from Lynn Miller at GCG.

>I was able to recreate this problem with the EPD database.
>On OSF/1 systems I consistantly see core dumps.  On other
>UNIX platforms I get varying results.  
>The problem seems to be with the calculation of the Z score.
>The Z score calculation is new starting with FASTA version 2.
>Since the FASTA in version 8.1 of the Wisconsin Package was 
>based on Dr. Pearson's version 1.7, and did not include these
>new statistical calculations, it makes sense that the search 
>works in this previous version.  I apologize that it no longer
>works in the current version.  The addition of statistical
>estimates to the fasta output was much-awaited, and has mainly
>had good effects.  Unfortunately, on some data sets, these
>calculations can cause problems.
>I have asked the developer to look more closely to see what is
>causing this specific problem.  In the meantime, you will
>not be able to use FASTA in version 9.0 or 9.1 to search
>the EPD database.  Instead, I suggest that you use a 
>non-statistically-based search program such as WordSearch.
>I personally do not feel that BLAST is a good option for searching
>this small database.
>You might also add that the statistical calculations in the
>newer version of FASTA were designed for databases containing a 
>large number of unrelated sequences, whereas EPD is a small
>database containing many similar sequences.
>Lynn Miller, Technical Support Coordinator

Aengus Stewart                          aengus.stewart at icrf.icnet.uk
Bioinformatics Support                  Tel: +44 (0)171 269 3679
Imperial Cancer Research Fund
Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK

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