EMBOSS: tfextract


Program tfextract

Function

Extract data from TRANSFAC

Description

Usage

Here is a sample session with tfextract.

% tfextract
Extract data from TRANSFAC
Full pathname of transfac SITE.DAT: /data/transfac/site.dat

Command line arguments

   Mandatory qualifiers:
  [-inf]               infile     Full pathname of transfac SITE.DAT

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-inf]
(Parameter 1)
Full pathname of transfac SITE.DAT Input file Required
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

The output from tfextract is a set of files in the emboss/data directory containing reformatted sites from the transfac database.

These files are used by the tfscan program to search for TRANSFAC sites in sequences.


% ls -1s emboss/data/tf*
 18 emboss/data/tffungi
 17 emboss/data/tfinsect
 56 emboss/data/tfother
  4 emboss/data/tfplant
112 emboss/data/tfvertebrate

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Program nameDescription
embossdataFinds or fetches the data files read in by the EMBOSS programs
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

Comments