[Bioperl-l] Purge command in SimpleAlign

[Aaron J Mackey]

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You have a multiple alignment of 40,000 sequences? <boggle> Surely there's
something you can do to cut out most of the (presumably) redundant
sequences before generating the alignment ... ?  Otherwise, I'd suggest a
hierarchical approach: subdivide your 40,000 sequences into (say) 400 sets
of 100 sequences each, apply the purge to each of the sets, and then start
combining, purging, combining, purging, etc.

- -Aaron

On Thu, 20 Dec 2001 jrest@umich.edu wrote:

> Concerning the purge function in SimpleAlign:
>
> "Function: removes sequences above whatever %id"
> "This function will grind on large alignments. Beware!"
> "(perhaps not ideally implemented)"
>
> This is true!  It worked great with 10, but with 40,000 sequences, it
> "grinds."
>
> Is there an alternative method someone can suggest to implement this
> function?  Are there any other pieces of code or software (perl or
> otherwise) to implement a "purge" (beside blast?)
>
> Thanks!
> Josh
>
>
>
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- -- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu

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