[Bioperl-l] correction to docs for Bio::SearchIO::axt
cjfields at uiuc.edu
Sat Sep 16 13:24:51 EDT 2006
Added it. Anything else?
On Sep 16, 2006, at 11:43 AM, Cathy Riemer wrote:
> Chris and Jason,
> Thanks for taking care of this. One small suggestion: to add the
> word "many" before "precomputed", since some sites might provide
> LAV (or other formats).
> On Sat, Sep 16, 2006 at 08:55:27AM -0500, Chris Fields wrote:
>> 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
>> in LAV format but are commonly post-processed to AXT format;
>> 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.
>> 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
>>>> 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 Riemer
>>>> Center for Comparative Genomics and Bioinformatics
>>>> Penn State University
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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