genewisedb - gene model options

Many of these options are identical to the genewise options listed above

-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.

-codon

[codon.table] Codon file -see genewise option

-gene

[human.gf] Gene parameter file - see genewise option

-subs

[1e-05] Substitution error rate - see genewise option

-indel

[1e-05] Insertion/deletion error rate - see genewise option

-cfreq

[model/flat] Using codon bias or not? [default flat] - see genewise option

-splice

[model/flat] Using splice model or GT/AG? [default model] - see genewise option

-intron

[model/tied] Use tied model for introns [default tied] - see genewise option

-null

[syn/flat] Random Model as synchronous or flat [default syn] - see genewise option

-alg

[421/623/2193/] Algorithm used for searching [default 623] The is the algorithm to use for the database search part of the process. 421 is the cheapest algorithm but can only be used with HMMs or small proteins as it has been compiled for a limited size of query. Looping algorithms (623L and 2193L) are not permitted as it is hard to interpret the results

-aalg

[623/623L/2193/2193L] Algorithm used for alignment [default 623/623L] This is the algorithm used for the alignment of the matches. The default for proteins is 623, whereas for HMMs it is the looping model 623L.

-kbyte

[ 2000] Max number of kilobytes used in alignments calculation. Maximum amount of memory allowed in the alignment process.

-cut

[20.00] Bits cutoff for reporting in search algorithm. Comparisons scoring greater than this cutoff are aligned.

-ecut

[n/a] Evalue cutoff only for searches which can calculate evalues

-aln

[50] Max number of alignments (even if above cut). A cutoff for the number of alignments, whatever their bits score.

-nohis

Don't show histogram on single protein/hmm vs DNA search. On a single protein (or hmm) vs DNA database search an on-the-fly evalue score is calculated. This disables the production of a histogram

-report

[0] Issue a report every x comparisons (default 0 comparisons). Mainly for debugging