[Bioperl-l] Running Smith Waterman alignments in BioPerl

Adam Witney awitney at sgul.ac.uk
Mon Mar 29 13:26:40 EDT 2010


thanks Chris for the explanation. It looks like Exonerate may also do something similar

thanks

adam


On 26 Mar 2010, at 15:51, Chris Fields wrote:

> It's not actively developed as far as I know.  I've been thinking that we could break it out of bioperl-ext and release it on it's own, with the intent that someone could take it up at some point.   We have started down that road with the HMM tools in bioperl-ext, though that one is still maintained by it's author.
> 
> I know many users just use calls to outside programs, such EMBOSS (which has water and needle) or others.  From the maintenance standpoint they're easier to update if something changes, XS can be a bugbear.
> 
> chris
> 
> On Mar 26, 2010, at 10:20 AM, Adam Witney wrote:
> 
>> Is the bioperl-ext package still being developed? I ask because i am looking at running some SW alignments using the pSW module, but the simple example in the pod gives the error 
>> 
>> "The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed.
>> Please read the install the bioperl-ext package"
>> 
>> even though i did compile and install the Bio::Ext::Align package
>> 
>> If not using the pSW module, what do other people use for this?
>> 
>> thanks
>> 
>> adam
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> 
> 
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