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)