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.