[Bioperl-l] Unusual behaviour of SeqIO::tigr

Josh Lauricha laurichj at bioinfo.ucr.edu
Mon Mar 8 14:38:33 EST 2004

On Mon 03/08/04 11:48, Morten Lindow wrote:
> Thanks Josh that helped,
> In case somebody else can use it I am pasting the complete code to get 
> the coordinates of all locations on one line each.
> But another thing: When parsing rice-pseudochromosome files I get a few 
> warnings like this(from around 20-30 sequences per chromosome):

Thats because not all of the proteins annotated are valid proteins.

> since the problem is only with a small fraction of the TUs I guess it is 
> not a bioperl problem, but rather a TIGR problem? Any comments?

TIGRs rice publications have some flaws that are slowly getting worked out.
The invalid proteins are one and there are still some examples where the
exon's are annotated to be outside of the TU their enclosed in.


| Josh Lauricha            | Ford, your turning into |
| laurichj at bioinfo.ucr.edu | a penguin. Stop it.     |
| Bioinformatics, UCR      |                         |
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