[WashU] HMMER
User's Guide


| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC|
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HMMER prior files

Observed counts of emissions (residues) and transitions (insertions and deletions) in a multiple alignment are combined with Dirichlet priors to convert them to probabilities in an HMM.

For protein models, by default, HMMER uses a nine-component mixture Dirichlet prior for match emissions, and single component Dirichlet priors for insert emissions and transitions. The nine-component match emission mixture Dirichlet comes from the work of Kimmen Sjölander [Sjölander et al., 1996].

For DNA/RNA models, by default, HMMER uses single component Dirichlets.

Two example null model files, amino.pri and nucleic.pri, are provided in the Demos subdirectory of the HMMER distribution. (They are copies of the internal default HMMER prior settings.)

The way the format of these files is parsed is identical to null models: everything after a # on a line is a comment, the order of occurrence of the fields is important, and fields must be separated by either blanks or newlines.

A prior file consists of the following fields:

In the code, prior files are parsed by prior.c:P7ReadPrior().


next up previous contents
Next: Sequence files Up: File formats Previous: HMMER null model files


Direct comments and questions to <eddy@genetics.wustl.edu>