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.