read blast output and mask query xblast xblast seqlab xblast perl "xblast" 0 blast_output Blast Output File (does not work on Blast2 or Blast-Wu output) perl " $value" 2 blast_output perl 1 query Query File perl " $value" 3 mask masking character perl " $value" 4 no value: will generate a query masked with 'x' N> will generate a query masked with 'N', etc ... for using special masking characters like '!@#$%^&*- =><' and others, quote them with '' for deleting instead of masking use empty double quotes : '' fasta generate a fasta-format database of the matched segments perl ($value)? " -d":"" 0 1 reversed generate a reversed output, e.g. masking the non-matched segments. perl ($value)? " -r":"" 0 1