[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 3. 102829.txt - Apparently a BioPerl error
> A 102829.gb file is an example

Read the error message, it tells you exactly what is wrong:

------------- EXCEPTION  -------------
MSG: 1 there is a conflict with exons; there was an explicitly stated  
exon with location 12..21, yet I cannot generate this e
xon from the supplied mRNA locations
1 There are some inferred exons that are not in the explicit exon  
list; they are the exons at locations:
25..447

STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/ 
perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
606
...


Then look at the GenBank file:

      gene            1..447
                      /gene="ESAG1"
      primer_bind     1..11
                      /gene="ESAG1"
      exon            <12..21
                      /gene="ESAG1"
                      /note="min-exon"
      CDS             25..>447
                      /gene="ESAG1"

I have to agree with the Unflattener, this doesn't make any sense at  
all.

Garbage in, garbage out.

-Aaron


--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
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