Description Usage Arguments Value Author(s) References Examples
Function for predicting the oligomeric state of a coiled-coil sequence
1 |
id |
A vector of id names for each sequence to be predicted |
seq |
A vector of amino acid sequences; where each element of the vector is a character string of amino-acid sequence. Valid characters are all uppercase letters except ‘B’, ‘J’, ‘O’, ‘U’, ‘X’, and ‘Z’; invalid characters will not be tolerated and their use will result in a failure of the program. |
reg |
A character string denoting the heptad register of each amino acid sequence;
valid characters are the lowercase letters ‘a’ to
‘g’. Register characters are not required to be in proper order.
The register can start with any of the seven letters.
It must always have the same length as the |
pssm |
A profile scoring matrix generated from the SCORER 2.0 training data. You can either use the default one or create your own PSSM using the pssm.R function |
delta |
A numeric value strictly superior to 0 that serves as pseudocount in the profile scoring matrix. Empirical analysis has shown that a value of delta=1 is optimal. |
The function scorer2
is the most important one in the
scorer2 package. It is used to apply the SCORER 2.0 prediction
algorithm to predict the oligomeric state of a new coiled-coil sequence.
By default the final classification is computed on the basis of
the discriminant function value. If f(x)>=0, x is
predicted as a dimer, otherwise as trimer.
Thomas L. Vincent tlfvincent@gmail.com
Craig T. Armstrong, Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. (2011) SCORER 2.0: an algortihm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics. DOI: 10.1093/bioinformatics/btr299
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