clasp - fast local fragment chaining using sum-of-pair gap costs
clasp [-fOmL] -i
reads tab-separated fragment files providing information
on fragment start and end position on query and database
sequence as well as a score measure.
It executes a fast local chaining algorithm using either
the linear or the sum-of-pair gap cost model. It produces a
tab-separated output file containing all necessary
information on the chains. Note that it is
optimized for short queries and large database sequences.
- -f, --fragments
- -O, --orig
Report fragments as given in input file.
- -m, --mute
- -L, --lin
Use linear gap cost model. By default, the sum-of-pair gap cost model is applied.
- -i, --input <file>
Filename of fragment input file.
- -o, --output <file>
Filename of output file. By default, the output is printed to the standard output.
- -c, --cols <qry_st> <qry_end> <db_st> <db_end> <score>
Select column numbers in input file corresponding to fragment start and end position on query and database sequence as well as a score measure. Note that column numbers are 1-based.
- -C, --idcols <n>...<n>
Select identifier columns. Only fragments with same entries in all identifier columns may be chained together. Note that column numbers are 1-based.
- -l, --lambda <double>
Gap cost parameter lambda. In case of the sum-of-pair gap cost model, the distance difference between adjacent fragments in chains on query and database sequence is penalized by
* distance difference. In case of the linear gap cost model, the distance on the database sequence between adjacent fragment in chains is punished by
* database distance.
- -e, --epsilon <double>
Gap cost parameter epsilon. In case of the sum-of-pair gap cost model, it penalizes the minimal distance between adjacent fragments in chains on either query or database sequence by
* database distance. In case of the linear gap cost model, the distance between adjacent fragment in chains on the query sequence is punished by
* query distance.
- -G, --maxgap <n>
Maximal allowed gap between adjacent fragments in any generated chain.
- -S, --minscore <double>
Minimal required score of chains to be reported.
- -F, --minfrag <n>
Minimal number of fragments in chains to be reported.
is free software for non-commercial use.
(C) 2009 Bioinformatik Leipzig
Please report bugs to <email@example.com>.