[Bioperl-l] correction to docs for Bio::SearchIO::axt

Jason Stajich jason at bioperl.org
Sat Sep 16 01:21:12 EDT 2006


right - I guess I meant the only way to get BLASTZ into our system is  
lav -> axt.

I will see if someone wants to update the module synopsis to clarify  
this point for users or I will get to it when I have time.

On Sep 15, 2006, at 11:18 PM, Cathy Riemer wrote:

> Hello Jason,
>
> I noticed an error in the documentation page for the
> Bio::SearchIO::axt parser at
> <http://search.cpan.org/~birney/bioperl/Bio/SearchIO/axt.pm>.
>
> The page states that "AXT format reports [are] typically produced
> by BLASTZ", but actually BLASTZ produces lav output, not axt.
> Sites that provide pre-computed BLASTZ alignments in axt format
> (such as UCSC's Genome Browser) convert them from lav to axt in
> a post-processing step.
>
> -Cathy
>
> ---
> Cathy Riemer
> Center for Comparative Genomics and Bioinformatics
> Penn State University



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