[EMBOSS] needle -nobrief

[Marc Logghe]

Great, thanks !

> -----Original Message-----
> From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk]
> Sent: Wednesday, March 19, 2008 10:29 AM
> To: Marc Logghe
> Cc: emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] needle -nobrief
> 
> 
> From a quick look at the code:
> 
> 
> Longest identity: you're right i.e.
> (Identical residues x 100)/(Length of Alignment - Total Number of Gaps
> in Alignment)
> 
> 
> 
> Shortest identity = number of identical residues * 100 /
>                     length of longest original sequence
> 
> 
> The similarity calculations are the same as the 'identical' ones
> except that the number of identical residues is replaced by the
> number of pairwise comparisons that have a positive score in
> the comparison matrix.
> 
> HTH
> 
> Alan
> 
> 
> 
> 
> > Hi all,
> >
> > I have checked the docs and googled around but I did not find an
> > explanation for how the shortest_similarity or shortest_identity is
> > calculated by needle (using the -nobrief option).
> >
> > For longest_identity it seems to be:
> >
> > (Identical residues x 100)/(Length of Alignment - Total Number of
Gaps
> > in Alignment)
> >
> > Thanks and regards,
> >
> > Marc
> >
> >
> >
> >
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>