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)