---
name: "libscan"
section: "1e"
platform: "linux"
package: "embassy-domainatrix"
version: "0.1.660-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/libscan"
---

# libscan(1e)

Diagnostic searches for protein families.

## 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.