NAME¶

SYNOPSIS¶

DESCRIPTION¶

If the original profile is given as the second argument, the normalization function specified within the profile will be updated such as to produce -Log10 per-residue E-values. If the second argument is omitted, the output consists of a header line containing the normalization parameters followed by a modified score list, showing original scores, normalized scores, and corresponding log-cumulative frequencies next to each other.

Note that this program implements the significance estimation procedure for profile match scores described in (Hofmann & Bucher 1995). It has been used for the calculation of the normalization parameters of all profiles in PROSITE.

PARAMETERS¶

L=#

Logarithmic base of the parameters of the estimated extreme-value distribution. The parameters reported by pfscale are expressed as logarithms and thus can be inserted directly into a linear normalization function defined in a generalized profile. Default: L=10.

N=#

Size of the database from which the input score list was derived. The searched database is typically a shuffled version of a real protein or nucleotide sequence database. Default: N=14147368 (size of SWISS-PROT release 30 and shuffled derivatives of it).

P=#

Upper threshold of the probability range to which the extreme-value distribution will be fitted. For instance: if N=10'000'000 and P=0.0001 (default value for P) then profile match scores below rank 1000 in the sorted input list (corresponding to occurrence probabilities > 0.0001) will be ignored.

Q=#

Lower threshold of the probability range to which the extreme-value distribution will be fitted. For instance: if N=10'000'000 and Q=0.000001 (default value for Q) then profile match scores above rank 10 in the sorted input list (corresponding to occurrence probabilities < 0.000001) will be ignored.

EXAMPLES¶

(1)

pfsearch -fr sh3.prf shuffle20.seq C=200 | sort -nr | pfscale - P=0.0001 Q=0.000001

derives score-normalization parameters for the SH3 domain profile in sh3.prf. shuffle20.seq contains a window-shuffled derivative of SWISS-PROT release 30 in Pearson/Fasta format (window-size 20). Note that the implicit default of N corresponds to the size of this database and thus needs not to be specified on the command line. The cut-off value C=200 will produce about 2000 matches completely covering the range defined by the command line parameters of P and Q. A suitable cut-off value has to be guessed in advance by computing a few optimal alignment scores for random sequences.

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AUTHOR¶