LIBSCAN(1e)						     EMBOSS Manual for Debian						       LIBSCAN(1e)

NAME

       libscan - Diagnostic searches for protein families.

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

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       libscan is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
	   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.

DOMAINATRIX 0.1.0+20100721					    08/11/2010							       LIBSCAN(1e)