ptoh - converts a PROSITE-formatted profile into an approximately
equivalent HMM
ptoh [ -fFhs ] [ profile-file | - ] [ random-model-file ] [L=#]
[I=#] [D=#]
ptoh converts a PROSITE-formatted generalized profile into
an approximately equivalent HMMER1- or SAM-formatted hidden Markov model
(HMM). profile-file is a nucleic acid or protein profile in PROSITE
format. random-model-file contains a simple null-model in the format
used by the HMM search programs of the HMMER1 package. The result is written
to the standard output.
The profile-to-HMM conversion method is described in Bucher et al.
(1996). All profile scores corresponding to transitions which are not
supported by the HMM architectures of the SAM and HMMER1 packages, are
ignored. If no random model is specified on the command line, the null model
given in the GENERAL_SPEC data block of the profile is used. If this is also
missing, a flat residue distribution is assumed.
- -f
- Generate free insert-modules (FIMs) at the beginning and at the end of the
model which approximately emulate domain-global or semi-global alignment
mode (see Bucher et al. 1996).
- -F
- Generate free insert-modules (FIMs) at the beginning and at the end of the
model which approximately emulate local alignment mode.
- -h
- Output in HMMER1 ascii format. This is the default.
- -s
- Output in SAM format.
- D=#
- Delete-to-delete transition probabilities used in conjunction with FIMs
(options -f, -F). This value will be imposed on all
delete-to-delete transitions of the model. The other outgoing transitions
from the affected delete states will be renormalized to satisfy the
"sum to one" requirement. Note that the application of the
D parameter precedes the application of the I parameter.
Delete-to-delete probabilities at the beginning and at the end of the
model may thus change again as a result of renormalizations following the
application of the I parameter. Default: D=0.9.
- I=#
- Insert-to-insert transition probabilities used in the FIMs ( see
options -f, -F). This value will be imposed on the first and the last
match-to-insert and insert-to-insert transition probabilities of the
model. The other outgoing transitions of the affected states will be
renormalized such as to satisfy the "summing to one"
requirement. If the -F option is simultaneously set, the I
parameter will also be imposed on the insert-to-delete transition
probability at the beginning, and on the delete-to-insert transition
probability at the end of the model. Default: I=0.99.
- L=#
- Logarithmic base used for conversion of the profile scores into HMM
probabilities (The profile scores are interpreted as log-odds ratios,
see Bucher et al. 1996). This value over-writes the logarithmic
base specified within the profile by the optional LOG_BASE
parameter. Default: 1.0233739 (1/30 bit units).
- (1)
- ptoh -Fs sh3.prf standard.random L=1.0233739 > sh3.hmm
Generates a SAM-formatted HMM for the SH3 domain from a
profile. sh3.prf contains the source profile in PROSITE format.
standard.random contains the null-model used for conversion of the
log-odds ratios into probabilities. The logarithmic base 1.0233739
corresponds to 1/30 bits, the implicit scale of the profile. The
-F option causes the HMM to emulate local alignment (fragment
search) mode.
Bucher P, Karplus K, Moeri N & Hofmann, K. (1996). A
flexible motif search technique based on generalized
profiles. Comput. Chem. 20:3-24.
Philipp Bucher
Philipp.Bucher@isrec.unil.ch