NAME

       gt-seed_extend - Calculate local alignments using the seed and extend algorithm.

SYNOPSIS

       gt seed_extend [option ...] encseq_basename [encseq_basename]

DESCRIPTION

       -ii [string]
           Input index for encseq encoded sequences

       -qii [string]
           Query input index (encseq)

       -seedlength [value]
           Minimum length of a seed default: logarithm of input length to the basis alphabet size

       -diagbandwidth [value]
           Logarithm of diagonal band width (for filter) (default: 6)

       -mincoverage [value]
           Minimum coverage in two neighbouring diagonal bands (for filter) default: 2.5 x
           seedlength

       -maxfreq [value]
           Maximum frequency of a k-mer (for filter) (default: undefined)

       -memlimit [string]
           Maximum memory usage to determine the maximum frequency of a k-mer (for filter)
           (default: undefined)

       -extendxdrop [value]
           Extend seed to both sides using xdrop algorithm, /noptional parameter specifies
           sensitivity (default: 97)

       -xdropbelow [value]
           Specify xdrop cutoff score (0 means automatically defined depending on minidentity)

       -extendgreedy [value]
           Extend seed to both sides using greedy algorithm, optional parameter specifies
           sensitivity (default: 97)

       -l [value]
           Minimum alignment length (for seed extension) (default: undefined)

       -minidentity [value]
           Minimum identity of matches (for seed extension) (default: 80)

       -a [value]
           show alignments/sequences (optional argument is number of columns per line) (default:
           70)

       -no-reverse [yes|no]
           do not compute matches on reverse complemented strand (default: no)

       -no-forward [yes|no]
           do not compute matches on forward strand (default: no)

       -v [yes|no]
           be verbose (default: no)

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

       Report bugs to <gt-users@genometools.org>.