Provided by: trnascan-se_1.3.1-1_amd64
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(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.
tRNAscan-SE(1), /usr/share/doc/trnascan-se/MANUAL.gz October 2015 COVELS(1)