covels - search DNA sequence databases for similar RNAs
Covariance models (CM's) are adaptive statistical models of the the secondary
structure and primary sequence consensus of an RNA family.
CM's are adaptive because a new model is learned from a set of example training
sequences. CM's are statistical because they embody a probabilistic
description of the consensus; mismatches, insertions, and deletions are
permitted, and the penalties paid are learned from the training sequences that
the model was constructed from.
covels -w 50 mymodel.cm /genbank/gbrna.seq
This command would search a database (here, a hypothetical GenBank structural
RNA database) and print scores and locations of all hits with positive scores
(i.e., good matches to the model). The difference between coves
is that covels
is a local search program instead of
global alignment; it will find optimal matches to subsequences in a long
sequence. The -w 50
parameter sets the maximum length of
match you expect to find (here, 50 bases). (The 'w' comes from ``window''; it
sets the size of the search scanning window.) This parameter affects the
running time and the memory consumption of covels
significantly, so you
want to set it as small as you can get away with.