GeneMark Manual

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Transition Matrices @MATDIR@

The GeneMark and GeneMark.hmm programs utilizes tables of oligonucleotide usage statistics as the basis for its coding potential function. These matrices are species specific. On this system, the matrix files have been installed in the directory @MATDIR@.

There may be more than one matrix available for an organism, often created to model classes of genes with distinct characteristics. The matrix you choose to use for gene-prediction will greatly affect your results so, here are some things to keep in mind:

GeneMark Matrices are Species Specific

It is sometimes possible to use matrices of one organism to predict coding regions in another. This works best if the organisms are phylogenetically very close.

If There Are Several Matrices for a Single Organism...

... then there are recognized more than one class of coding region in that organism. Often the coding regions will simply be classified by coding potential, but classifications may also be based on statistical clustering. If you are not sure which matrix is appropriate, try both.

If There Is No Appropriate Matrix for Your Organism...

... you have several options:

Use MkMat to create a new matrix for your organism

Try and use a matrix designed for a similar organism

Look for a new matrix for your organism (a current collection of GeneMark matrix files can be found on the WWW at )

Contact Gene Pro, Inc. about creating a new matrix for you . We are happy to work with you in generating a matrix for your organism. We like do this on a case-by-case basis so as to best accomodate your specific situation.

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