I am not sure I understand your question, and I will assume that by
"normal set of these parameters" you mean "unifying set across
different programs". If that's your question, the answer is that
there is no common set of lambda and kappa parameters (extreme value
distribution factors) between different programs, or even within the
same program. The values of these parameters are dependent on the
scoring scheme used, so when you change the substitution matrix in
PSI-BLAST, they will change. If you calibrate HHPRED models in
"local" and "global" modes, you'll get different kappa and lambda
values, and the same is true if you change other program parameters
that affect the scoring and alignments. If you take a sequence (or
profile) with certain composition and length and calculate lambda and
kappa, they will be different from the next sequence depending on its
length and sequence composition. In an extreme case, you can even
take the same HHPRED profile and calibrate it against two different
databases, for example the one provided with the program, and another
database with similar number of profiles, and you'll most likely get
different extreme value distribution parameters. Before anyone freaks
out because of this uncertainty, it bears mentioning that most of
these changes would affect only borderline matches.
This is to say that you can't determine these parameters in one
program and then use them with others. You can't even determine these
parameters for local scoring and then use them for global scoring
with the same program. In short, extreme value distribution
parameters are both sequence-, program- and scoring parameter-specific.
Hope this helps,
Mensur
At 12:16 AM 2/9/2012, you wrote:
Dear Modellers,
For E-value and alignment scoring systems, we use the parameters
lambda and K.
Specifying these scores is must for a scoring system. So what is/are
the normal set of these parameters used in PSI-BLAST/CS-BLAST/HHPRED
or other profile inclusion based template searching methods?
Tell me the commonly used values for these two parameters lambda and
K for the calculation of alignment scores.
Thanks
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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