[R] BLAST output parsing

[A.J. Rossini]

One alternative can be found in my under development (slow, and
probably won't be finished) BioSeq1 package; it can be gotten
painfully via:

          http://www.bioconductor.org/develPage/develPackages.html

There are tools for getting BLAST results back and processing them.

best,
-tony

Tom Blackwell <tblackw at umich.edu> writes:

> Matt  -
>
> Yes, you would be seriously re-inventing the wheel.
> A standard tool is the  bioperl SearchIO  package.
> This is described at
>
> www.bioperl.org > Docs > SearchIO HOWTO:
>
> The html version of that link evaluates to:
>
> http://bioperl.org/HOWTOs/html/SearchIO.html
>
> -  best  -  tom blackwell  -  u michigan medical school  -  ann arbor  -
>
> On Fri, 19 Mar 2004, Matthew Oliver wrote:
>
>> Hi All,
>>
>> I have use the BLAST program provided by NCBI to compare large databases and have
>> generated a lot of output in one long text file. I was looking for a way to parse
>> out the results in a nice way so that it could be easily visualized. I was thinking
>> of trying to write something in R, but I wanted to check in with the help group to
>> make sure I am not re-inventing the wheel. Any help would be great!
>>
>> Matt Oliver
>>
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>
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-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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