[Bioperl-l] Meaning of Scores and Sample code for Bio::Matrix::Scoring

Wijaya Edward ewijaya at i2r.a-star.edu.sg
Fri Sep 8 05:34:43 EDT 2006


Hi,
 
Where can I find further information 
on the meaning of the value returns by Bio::Matrix::Scoring
functions.
 
For example, I would like to know 
what is the meaning of these scores,
and how was it calculated.
 
1. expected_score
2. Lambda  (is this the prior probablity of a substring
    generated according to background input sequence probability
     or something else?)
 
And what are the value we should pass for them.
e.g. it is not clear to me what does $newval refer to
in this context: 
 
$obj->expected_score($newval)
 
Perhaps a pointer of sample script that uses these
score can be useful also.
 
The information provided in the doc is quite minimum.
 
 
Regards,
Edward WIJAYA
SINGAPORE

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