Common options to change

There are a number of common options that can be used. Options can be issued anywhere on the command line.

-help

help on options

-version

show version and build date (useful for bug reporting)

-quiet

remove update line on stderr and informational messages

-silent

suppress all messages to stderr

-report

number for database searching, issue a report on stderr every number of comparisons (useful to ensure it is actually running)

-trev

genewise and estwise - use the reverse strand of the DNA

-both

genewise and estwise - use both strands of the DNA

-u position

The start point in the DNA sequence for the comparison

-v position

The end point in the DNA sequence for the comparison

-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.

-gene file

change gene model parameters. Currently we have either human (human.gf) or worm (worm.gf)

-genes

Output option for genewise algorithms - show an easy to read gene structure report

-trans

Output option for genewise algorithms - provide an automatic translation of the predicted gene as a fasta format

-cdna

Output option for genewise algorithms - provide an automatic construction of the spliced dna sequence as a fasta format

-ace

Output option for genewise algorithms - provide an ACeDB subsequence model output