libscan1e
Diagnostic searches for protein families.
Usage
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
Overview
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
Releases
Unchanged in 7 releases since Debian 7 (Wheezy).