[Bioperl-l] Alignment

Chris Fields cjfields at uiuc.edu
Tue Feb 20 10:49:56 EST 2007

On Feb 20, 2007, at 9:30 AM, Albert Vilella wrote:

> I think the SimpleAlign object contains a set of sequences, each of
> which is a LocatableSeq object.
> These LocatableSeq objects will have gaps, represented by '-' or
> whatever other symbol is specified (I think there are methods for it),
> and then one can use methods like column_from_residue_number to map
> the coordinates between the primary sequence and the aligned sequence.
> The perldoc for LocatableSeq has some examples on how to use these
> methods.
> [Hopefully I haven't written any lie in this message],
> Cheers,
>     Albert.

No lies.  The comparison methods are in SimpleAlign; if you look in  
SimpleAlign.t you'll see several demos on how to go abouot adding  
LocatableSeqs to a SimpleAlign object and then use SimpleAlign  
methods for them.


PS (to marian): I'm a bit behind this week, so the bracket_strings  
stuff is lagging behind; I'm writing up some stuff on a deadline.

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