[Bioperl-l] Sequence features - complete sequences

[Jason Stajich]

This is encoded in the Location object. In fact if the location is not 
exact we create a "fuzzy" location, you can just test if it is-a 
Bio::Location::FuzzyLocationI.

More properly (if you only cared about proteins that were incomplete in 
C-terminus or N-terminus) - You just need to check the  start_pos_type 
and  end_pos_type of the location. If they are 'EXACT' then the 
position is, well, exact.
if( $f->location->start_pos_type eq 'EXACT' && 
$f->location->end_pos_type eq 'EXACT' ) {
}

-jason
On Jan 19, 2005, at 7:52 AM, Paulo Almeida wrote:

> That's what I thought, but I don't want the rest of the information; I
> just want to skip those sequences, because I am using them to generate
> ProtDist matrices, and they may distort the results.
>
> -Paulo
>
>> I think in a lot of cases this means that there _is_ more sequence in 
>> _reality_, but not available in the databases (e.g. not a full length 
>> cDNA clone). Just because that part was never isolated and thus, not 
>> sequenced. Meaning there is no way to fetch the missing sequence 
>> information.
>> Regards,
>> Marc
>
> -- 
> Paulo Almeida
> Instituto Gulbenkian de Ciencia
> Apartado 14, 2781-901, Oeiras, PORTUGAL
> tel  +351 21 446 46 35
> fax  +351 21 440 79 70
> http://www.igc.gulbenkian.pt
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/