This is the command gt-seed_extend that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 <[email protected]>.
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