SYNOPSIS

libscan -mode list -grib boolean -henik boolean -hmm boolean -sam boolean -pssm boolean -sig boolean -hmmpath string -hmmextn string -hmmoutpath string -hmmoutextn string -sampath string -samextn string -samoutpath string -samoutextn string -pssmpath string -pssmextn string -niter integer -thresh float -maxhit integer -pssmoutpath string -pssmoutextn string -gbvpath string -gbvextn string -gbvgapo float -gbvgape float -gbvoutpath string -gbvoutextn string -hnfpath string -hnfextn string -hnfgapo float -hnfgape float -hnfoutpath string -hnfoutextn string -sigpath string -sigextn string -nterm list -sub matrixf -siggapo float -siggape float -sigoutpath string -sigoutextn string -db seqset -scopf infile

libscan -help

DESCRIPTION

libscan

is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Protein:3D Structure" command group(s).

OPTIONS

-mode list

libscan runs in one of two modes either (i) database search mode or (ii) library screen mode. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top-scoring families) for each one. Default value: 2

-grib boolean

Default value: N

-henik boolean

Default value: N

-hmm boolean

Default value: N

-sam boolean

Default value: N

-pssm boolean

Default value: Y

-sig boolean

Default value: N

-hmmpath string

Default value: ./lib/

-hmmextn string

Default value: .hmm

-hmmoutpath string

Default value: ./

-hmmoutextn string

Default value: .hmmout

-sampath string

Default value: ./

-samextn string

Default value: .mod

-samoutpath string

Default value: ./

-samoutextn string

Default value: .samout

-pssmpath string

Default value: /data/structure/lib/pssm/

-pssmextn string

Default value: .chk

-niter integer

Default value: 1

-thresh float

Default value: 100

-maxhit integer

Default value: 1000

-pssmoutpath string

Default value: ./

-pssmoutextn string

Default value: .pssmout

-gbvpath string

Default value: ./

-gbvextn string

Default value: .grib

-gbvgapo float

Default value: 10.0

-gbvgape float

Default value: 0.5

-gbvoutpath string

Default value: ./

-gbvoutextn string

Default value: .gribout

-hnfpath string

Default value: ./

-hnfextn string

Default value: .henik

-hnfgapo float

Default value: 10.0

-hnfgape float

Default value: 0.5

-hnfoutpath string

Default value: ./

-hnfoutextn string

Default value: .henikout

-sigpath string

Default value: ./

-sigextn string

Default value: .sig

-nterm list

Default value: 1

-sub matrixf

Default value: EBLOSUM62

-siggapo float

Default value: 10.0

-siggape float

Default value: 0.5

-sigoutpath string

Default value: ./

-sigoutextn string

Default value: .sigout

-db seqset

In database search mode libscan scans each discriminating element against a sequence set. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) Default value: 49142.vdhf

-scopf infile

In either mode, a 'scop classification file' is required as a source of family classification data. A scop classification file contains classification and other data for domains from the scop database. The file is in embl-like format and is generated by scopparse. Domain sequence information can be added to the file by using scopseqs. Default value: /data/structure/dcf/scop_raw.dcf

AUTHOR

Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.