[Biojava-l] Restriction Enzyme Support

Schreiber, Mark mark.schreiber@agresearch.co.nz
Fri, 21 Jun 2002 08:56:17 +1200

I'd say suffix trees would be the way to do it quickly.

- Mark

> -----Original Message-----
> From: Keith James [mailto:kdj@sanger.ac.uk] 
> Sent: Thursday, 20 June 2002 8:47 p.m.
> To: Schreiber, Mark
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Restriction Enzyme Support
> >>>>> "Mark" == Schreiber, Mark <mark.schreiber@agresearch.co.nz> 
> >>>>> writes:
>     Mark> Hi - I don't believe that there is, although conceivably one
>     Mark> wouldn't be hard to make and would probably be quite
>     Mark> useful. Anyone interested in making one could probably take
>     Mark> a lead from the proteomics package and the protease
>     Mark> digestion classes. Any takers?
> I'll have a go at this - I've done enough real restriction 
> digests in my time. Some virtual ones won't hurt.
> The BioJava Protease class does its "cutting" by annotating 
> Features onto the target sequence. This is just one of the 
> conceptual "cutting" mode which springs to mind:
> 1. report the locations of cuts
> 2. annotate features representing the product fragments
> 3. return a set of actual product fragments as new objects
> I've just had a look at the BioPerl RestrictionEnzyme class 
> which nicely does all three. I'd say that's a suitable 
> reference point for a good implementation - I'll aim for a 
> similar API.
> Given that we are using SymbolLists and not chars, regexes 
> are out of the picture. So how to make this efficient for big 
> sequences? The protease class uses a simple scan down the 
> sequence, but given typical use cases for RE digests (scan 
> many Kb/Mb with potentially hundreds of
> enzymes) I don't think the performance would be acceptable.
> With a bit of test code I found that I can quickly obtain all 
> motifs up to n residues long using the SuffixTree class, but 
> I haven't quite figured out how to map their locations back 
> to the SymbolList. After this is done we can find ambiguous 
> matches using BasisSymbols. Does that sound like a reasonable 
> approach?
> Keith
> -- 
> -= Keith James - kdj@sanger.ac.uk - 
> http://www.sanger.ac.uk/Users/kdj =- Pathogen Sequencing 
> Unit, Wellcome Trust Sanger Institute, Cambridge, UK
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