| ## EMBOSS: helixturnhelix

# Program helixturnhelix

## Function

Report nucleic acid binding motifs

## Description

helixturnhelix uses the method of Dodd and Egan and finds helix-turn-helix nucleic acid binding motifs in proteins.

The helix-turn-helix motif was originally identified as the DNA-binding domain of phage repressors. One alpha-helix lies in the wide groove of DNA; the other lies at an angle across DNA.

## Usage

Here is a sample session with helixturnhelix.

    % helixturnhelix
    Input sequence: sw:laci_ecoli
    Output file [laci_ecoli.hth]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outfile]           report     (no help text) report value

       Optional qualifiers:
       -mean               float      Mean value
       -sd                 float      Standard Deviation value
       -minsd              float      Minimum SD
       -eightyseven        bool       Use the old (1987) weight data

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outfile] (Parameter 2) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
-mean | Mean value | Number from 1.000 to 10000.000 | 238.71
-sd | Standard Deviation value | Number from 1.000 to 10000.000 | 293.61
-minsd | Minimum SD | Number from 0.000 to 100.000 | 2.5
-eightyseven | Use the old (1987) weight data | Yes/No | No
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The input sequence can be one or more protein sequences.

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default helixturnhelix writes a 'motif' report file.

Here is a sample output:

    ########################################
    # Program: helixturnhelix
    # Rundate: Mon Feb 11 13:45:02 2002
    # Report_file: laci_ecoli.hth
    ########################################

    #=======================================
    #
    # Sequence: LACI_ECOLI     from: 1   to: 360
    # HitCount: 1
    #
    # Hits above +2.50 SD (972.73)
    #
    #=======================================

    Maximum_score_at at "*"

    (1) Score 2160.000 length 22 at residues 4->25
               *
     Sequence: VTLYDVAEYAGVSYQTVSRVVN
               |                    |
               4                    25
     Standard_deviations: 6.54

    #---------------------------------------
    #---------------------------------------

## Data files

The data files are stored in the standard EMBOSS data directory. The names are:

- Ehth.dat matrix file
- Ehth87.dat 1987 shorter matrix file

With care these can be replaced to suit your data sets. If the files are placed in the following directories they will be used in preference to the files in the EMBOSS distribution data directory:

- . (your current directory)
- .embossdata
- ~/ (your home directory)
- ~/.embossdata

Here is the default file:

    # Amino acid counts for 91 Helix-turn-helix (presumed) protein motifs
    # from Dodd IB and Egan JB (1990) Nucl. Acids. Res. 18:5019-5026.
    #
    Sample: 91 aligned sequences
    #
    # R  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 Total Exp
    # - -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- ----- ---
      A  2  1  3 14 10 12 75  6 15  9  1  1  4  3  8 15  4  4  4 11  0 10   212 995
      C  0  0  1  1  0  0  0  0  0  3  3  1  1  0  0  0  0  0  0  1  0  3    14 106
      D  0  1  0  1 14  0  0 14  1  0  5  0  1  2  0  0  0  0  1  1  0  2    43 556
      E  4  5  0 11 26  0  0 16  9  3  3  0  3 12 13  0  0  2  0  1 13  6   127 669
      F  4  0  4  0  0  4  0  1  0 10  0  0  0  0  1  0  0  1  1  1 22  0    49 358
      G  9  7  1  4  0  0  8  0  0  0 50  0  6  0  7  1  0  3  1  1  0  4   102 761
      H  4  3  1  1  2  0  0  3  2  0  5  0  3  3  0  2  0  2  4  5  0  2    42 225
      I 10  0 13  3  2 15  0  4  9  4  0 17  0  2  0  1 31  1  4  8 16  1   141 583
      K  4  4  6 11 12  1  1 14 11  0  5  2  2  7  2  1  0  5  8  4  5 15   120 516
      L 16  1 17  0  1 35  0  3 12 31  0 22  0  2  1  1 22  1  1 12 20  0   198 954
      M  7  0  2  1  1  1  0  0  5  7  1 10  0  0  2  0  2  0  0  2  0  1    42 275
      N  0  8  0  1  0  0  0  2  1  1 14  0  8  1  4  2  0  4  9  0  0 11    66 383
      P  1  6  0  1  0  0  0  0  0  0  0  0  3 13  7  0  0  0  0  0  0  3    34 403
      Q  2  1 21  9 11  0  0  9  8  0  0  2  1 17  7 12  0  3 12  5  3  9   132 437
      R  9 10 14  9  5  0  1 16 10  0  1  0  1 17  8  7  0 17 28  3  0 16   172 609
      S  2 17  0  8  4  1  6  1  2  2  3  0 37  1 25  5  0 29  3  0  1  5   152 552
      T  6 24  3 12  1  5  0  2  2  4  0  5 20  4  3 39  0  4  1  0  4  3   142 512
      V  7  3  1  1  2 16  0  0  2 12  0 29  0  5  3  3 32  0  7  8  7  0   138 724
      W  2  0  0  0  0  0  0  0  0  1  0  1  0  0  0  0  0  0  2 21  0  0    27 105
      Y  2  0  4  3  0  1  0  0  2  4  0  1  1  2  0  2  0 15  5  7  0  0    49 267

## Notes

None.

## References

1. Dodd I.B., Egan J.B. (1987) "Systematic method for the detection of potential lambda cro-like DNA-binding regions in proteins." J. Mol. Biol. 194: 557-564.
2. Dodd I.B., Egan J.B. (1990) "Improved detection of helix-turn-helix DNA-binding motifs in protein sequences." Nucleic Acids Res. 18: 5019-5026.

## Warnings

The program will warn you if the data file is not mathematically accurate.

## Diagnostic Error Messages

None.

## Exit status

It exits with status 0 unless an error is reported.

## Known bugs

None.

## See also

Program name | Description
--- | ---
antigenic | Finds antigenic sites in proteins
digest | Protein proteolytic enzyme or reagent cleavage digest
fuzzpro | Protein pattern search
fuzztran | Protein pattern search after translation
garnier | Predicts protein secondary structure
hmoment | Hydrophobic moment calculation
oddcomp | Finds protein sequence regions with a biased composition
patmatdb | Search a protein sequence with a motif
patmatmotifs | Search a PROSITE motif database with a protein sequence
pepcoil | Predicts coiled coil regions
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
preg | Regular expression search of a protein sequence
pscan | Scans proteins using PRINTS
sigcleave | Reports protein signal cleavage sites
tmap | Displays membrane spanning regions

## Author(s)

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

Original program "HELIXTURNHELIX" by Peter Rice (EGCG 1990)

## History

Completed 11th March 1999

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments