Provided by: cassiopee_1.0.9-1_amd64
cassiopee - index and search tool in genomic sequences
cassiopee [Options] <sequence>
Cassiopee index and search library C implementation. It is a complete rewrite of the ruby Cassiopee gem. It scans an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions.
-l: maximum index depth / maximum pattern size -u: save index for later use -s: sequence to index -p: pattern to search -f: file containing pattern to search -o: output file -r: apply tree reduction -m: search mode: 0=DNA, 1=RNA, 2=Protein -a: allow alphabet ambiguity search -n: max consecutive N allowed matches in search -e: max substitution allowed matches in search -i: max indel allowed matches in search -g: generates a dot file of the graph -d: max depth of the graph -t: output format: 0:tsv (default), 1:json -x: minimum position in sequence -y: maximum position in sequence -v: show version -h: show this message