libscan - Diagnostic searches for protein families.

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       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).

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
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DOMAINATRIX 0.1.0+20100721                         08/11/2010                                        LIBSCAN(1e)

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).

       libscan - Diagnostic searches for protein families.

-modelist
           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

       -gribboolean
           Default value: N

       -henikboolean
           Default value: N

       -hmmboolean
           Default value: N

       -samboolean
           Default value: N

       -pssmboolean
           Default value: Y

       -sigboolean
           Default value: N

       -hmmpathstring
           Default value: ./lib/-hmmextnstring
           Default value: .hmm

       -hmmoutpathstring
           Default value: ./

       -hmmoutextnstring
           Default value: .hmmout

       -sampathstring
           Default value: ./

       -samextnstring
           Default value: .mod

       -samoutpathstring
           Default value: ./

       -samoutextnstring
           Default value: .samout

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

       -pssmextnstring
           Default value: .chk

       -niterinteger
           Default value: 1

       -threshfloat
           Default value: 100

       -maxhitinteger
           Default value: 1000

       -pssmoutpathstring
           Default value: ./

       -pssmoutextnstring
           Default value: .pssmout

       -gbvpathstring
           Default value: ./

       -gbvextnstring
           Default value: .grib

       -gbvgapofloat
           Default value: 10.0

       -gbvgapefloat
           Default value: 0.5

       -gbvoutpathstring
           Default value: ./

       -gbvoutextnstring
           Default value: .gribout

       -hnfpathstring
           Default value: ./

       -hnfextnstring
           Default value: .henik

       -hnfgapofloat
           Default value: 10.0

       -hnfgapefloat
           Default value: 0.5

       -hnfoutpathstring
           Default value: ./

       -hnfoutextnstring
           Default value: .henikout

       -sigpathstring
           Default value: ./

       -sigextnstring
           Default value: .sig

       -ntermlist
           Default value: 1

       -submatrixf
           Default value: EBLOSUM62

       -siggapofloat
           Default value: 10.0

       -siggapefloat
           Default value: 0.5

       -sigoutpathstring
           Default value: ./

       -sigoutextnstring
           Default value: .sigout

       -dbseqset
           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

       -scopfinfile
           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

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

libscan-modelist-gribboolean-henikboolean-hmmboolean-samboolean-pssmboolean-sigboolean-hmmpathstring-hmmextnstring-hmmoutpathstring-hmmoutextnstring-sampathstring-samextnstring-samoutpathstring-samoutextnstring-pssmpathstring-pssmextnstring-niterinteger-threshfloat-maxhitinteger-pssmoutpathstring-pssmoutextnstring-gbvpathstring-gbvextnstring-gbvgapofloat-gbvgapefloat-gbvoutpathstring-gbvoutextnstring-hnfpathstring-hnfextnstring-hnfgapofloat-hnfgapefloat-hnfoutpathstring-hnfoutextnstring-sigpathstring-sigextnstring-ntermlist-submatrixf-siggapofloat-siggapefloat-sigoutpathstring-sigoutextnstring-dbseqset-scopfinfilelibscan-help