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

[Brian Desany]

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:

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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.