CLASP


NAME

clasp - fast local fragment chaining using sum-of-pair gap costs

SYNOPSIS

clasp [-fOmL] -i file [ -o file ] [-c qry_st qry_end db_st db_end score ] [-C n...n ] [-l double ] [-e double ] [-G n ] [-S double ] [-F n ]

DESCRIPTION

clasp 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.

OPTIONS

-f, --fragments
Report fragments.
-O, --orig
Report fragments as given in input file.
-m, --mute
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 lambda * distance difference. In case of the linear gap cost model, the distance on the database sequence between adjacent fragment in chains is punished by lambda * 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 epsilon * database distance. In case of the linear gap cost model, the distance between adjacent fragment in chains on the query sequence is punished by epsilon * 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.

REFERENCES

clasp is free software for non-commercial use.
(C) 2009 Bioinformatik Leipzig

BUGS

Please report bugs to <christian@bioinf.uni-leipzig.de>.