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

Chris Fields cjfields at uiuc.edu
Sat Sep 16 09:55:27 EDT 2006


Jason, Cathy,

I changed the POD description to the following in CVS:

....

=head1 DESCRIPTION

This is a parser and event-generator for AXT format reports.  BLASTZ
reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally
in LAV format but are commonly post-processed to AXT format; precomputed
BLASTZ reports, such as those found in the UCSC Genome
Browser, are in AXT format.   This parser will also parse any
AXT format produced from any lav report and directly out of BLAT.
...


Chris

On Sep 16, 2006, at 12:21 AM, Jason Stajich wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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