[Jalview-discuss] what does quality refer to in annotation of the alignment?

[Deniz Erturk]

That helps, thanks Jim.
Deniz

> Date: Mon, 12 May 2008 22:25:44 +0100
> From: jimp at compbio.dundee.ac.uk
> To: jalview-discuss at jalview.org
> Subject: Re: [Jalview-discuss] what does quality refer to in annotation of	the	alignment?
> 
> Hi Deniz, sorry - I left you hanging here (I guess I was hoping someone
> else might reply!).
> 
> Deniz Erturk wrote:
> > Does anyone know what does "quality " exactly refer to in annotation of
> > an alignment?
> Its described in the online help (here:
> http://www.jalview.org/help/html/calculations/quality.html) - basically
> the height of the histogram at each alignment position reflects the cost
> of all residue substitutions observed in the column relative to the the
> sum of BLOSUM62 scores that would be obtained if the column were
> completely conserved. I don't have a precise reference to hand
> concerning this score, but its certainly not novel and is in essence a
> local multiple sequence alignment objective function.
> 
> does that help ?
> Jim
> 
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