genewise - options: dna/protein

-u

start position in dna

-v

end position in dna

-trev

Compare on the reverse strand

-tfor

(default) Compare on the forward strand

-both

Both strands

-tabs

Report positions as absolute to truncated/reverse sequence

-s

start position in protein - has no meaning for HMMs

-t

end position in protein - has no meaning for HMMs

-gap

[no] default [12] gap penalty to use for protein comparisons. This is used to estimate a probability per gap

-ext

[no] default [2] extension penalty to use for protein comparisons. This is used to estimate a probability for an extension of a gap

-matrix

default [blosum62.bla] Comparison matrix. Must be in half-bit units (blosum62 is in half bits). This is used to estimate a probability of amino acid comparisons

-hmmer

Protein file is HMMer 2 HMM

-hname

Use this as the name of the HMM.

-init

[default/global/local/wing] (see section 4.3.3) For protein sequences the default is to be local (like smith waterman). For protein profile HMMs, the default is read from the HMM - the HMM carries this information internally. The global mode is equivalent to to the ls building option (the default in the HMMer2 package). The local mode is equivalent to to the fs building option (-f) in the HMMer2 package. The wing model is local on the edges and global in the middle.