[Bioperl-l] RE: not all sequence is created equal (base quality d

[Jason Stajich]

Oh - definitely - I'm much more interested in adding phred quality scores to
sequence than dealing with PIR's notion of quality, I just started thinking
about it again (back burnered) when trying to solve the simple problem of
parsing PIR files.

I'm most interested in developing a way to couple the quality 'sequence' as
you implemented with a dna/protein sequence in a fairly succient way.  Would
love to have your code as a starting point once we all agreed on an
architecture design.

-Jason

----- Original Message -----
From: "Brian Desany" <bdesany@bcm.tmc.edu>
To: <bioperl-l@bioperl.org>
Sent: Thursday, June 28, 2001 11:52 AM
Subject: [Bioperl-l] RE: not all sequence is created equal (base quality d


> As someone doing nucleotide sequencing, I can say that our notion of
quality
> is very different from the PIR example you have. For us, each base has a
> quality value (called by phred). It is typically represented in a
fasta-like
> format such that you have a comment line and then the data consists of
> space-delimited numbers, one per corresponding base. So I think adding a
> Quality object to the sequence makes the most sense from this perspective.
> In fact I've hacked my copy of bioperl to have "qual" as an additional
> sequence type in PrimarySeq, and I created Bio::SeqIO::qual (and
> Bio::Index::Qual ) to support it, if anyone thinks that might be useful.
> However note that the implementation treats a "quality entity" as just
> another sequence type (i.e. dna, protein, quality) as opposed to something
> that is associated with it's pair (i.e. like a qual object associated with
a
> seq object).
>
> -Brian.
>
> Original message:
>
> --__--__--
>
> Message: 1
> Date: Wed, 27 Jun 2001 16:05:25 -0400 (EDT)
> From: Jason Stajich <jason@chg.mc.duke.edu>
> To: Bioperl <bioperl-l@bioperl.org>
> Subject: [Bioperl-l] not all sequence is created equal (base quality data)
>
> It would obviously be of interest to our friends doing sequencing as
> well as our friends doing prediction and other analysis who want to
> weigh low quality sequence less if we could incorperate base quality
> information into the idea of Sequence somehow.
>
> etc.
>
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