NAME

       covels - search DNA sequence databases for similar RNAs

DESCRIPTION

       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.

EXAMPLE

       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(1) and covels 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.

SEE ALSO

       tRNAscan-SE(1), /usr/share/doc/trnascan-se/MANUAL.gz

                                                  October 2015                                         COVELS(1)