Scroll to navigation

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.
08/11/2010 DOMAINATRIX 0.1.0+20100721