[Bio-software] Re: Clustal percent identity matrix
(by darek.kedra from gmail.com)
Tue Aug 12 08:12:23 EST 2008
On Aug 8, 2:23 am, arun iyer <iyerar... from yahoo.com> wrote:
> I was wondering if the % identity matrix in clustal is actually useful to assign an bacteria as a distinct species.
> I ran an multiple alignment for DNA using default parameters. the % identity matrix shows that the 2 organisms is 97% identical. The absoulute nucleotide identity is 99%.
> the % ID matrix is generated after penalties...but is it really useful?
What are your DNA sequences? It does not make sense to speak about %
identity without knowing what you compare to what. Human and chimp
differ more on nucleotide level among many coding sequences. Two
different copies of genome of the same, presumably single organism may
differ much more, i.e Ciona.
So it all depends
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