Helixturnhelix

• HELIXTURNHELIX
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • ALGORITHM
  • INPUT FILE
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES
  • OPTIONAL PARAMETERS
    • -MINSD
    • -TESTMEAN
    • -TESTSD
    • -MONitor
  • REFERENCES

HELIXTURNHELIX

FUNCTION

HelixTurnHelix uses the method of Dodd and Egan to determine the significance of possible helix-turn-helix matches in protein sequences.

DESCRIPTION

HelixTurnHelix uses the Dodd and Egan matrix to test for the presence of a helix-turn-helix DNA-binding motif in a protein sequence.

AUTHOR

This program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with HelixTurnHelix

  
  
  % helixturnhelix
  
   HELIXTURNHELIX uses protein sequences
  
   HELIXTURNHELIX of what sequence(s) ?  Sw:Laci_Ecoli
  
        Start (* 1 *) ?
      End (*   360 *) ?
  
   What should I call the output file (* laci_ecoli.hth *) ?
  
  %
  

OUTPUT

The output from HelixTurnHelix is a file containing the highest scoring hit, and all the hits above a standard deviation threshold.

  
  
  HELIXTURNHELIX of sw:laci_ecoli from: 1 to: 360
  
  Using distribution mean: 238.71 and SD: 293.61
  
  Report scores beyond +2.50 standard deviations
  
  Hits above +2.50 SD (972.73)
  
  Score 2202 (+6.69 SD) in SW:LACI_ECOLI at residue 5
  P03023 escherichia coli. lactose operon repressor. 8/91
  
   Sequence:  TLYDVAEYAGVSYQTVSRVVNQ
         |                    |
         5                    26
  
  

ALGORITHM

HelixTurnHelix uses the method of Dodd IB and Egan JB (1990) Nucl. Acids. Res. 18:5019-5026, an update of the method in Dodd IB and Egan JB (1987) J Mol Biol 194:557-664.

INPUT FILE

The input file for HelixTurnHelix is one or more GCG protein sequence files.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum syntax: % helixturnhelix [-INfile=]Sw:Laci_Ecoli -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=346              Range of interest
  -OUTFILE=laci_ecoli.hth        Output file
  
  Local Data Files:
  
  -DATa=doddegan.dat           Older version of matrix
  -EIGHTYSEVEN                 Use DoddEgan87.Dat
  
  Optional Parameters:
  
  -MINSD=2.5                     Show all hits over 2.5 SDs above mean
  -TESTMEAN=238.71               Mean score for non-HTH proteins
  -TESTSD=293.61                 Standard deviation for non-HTH proteins
  

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

The frequency table is stored in file doddegan.dat. You can Fetch this table and edit it (for example to include additional motif sequences). HelixTurnHelix will insist that each column has the same total.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-MINSD=2.5

shows all hits at this number of standard deviations above the mean.

-TESTMEAN=238.71

defines the mean score for a test run against a set of non-HTH proteins.

-TESTSD=293.61

defines the standard deviation for a test run against a set of non-HTH proteins.

-MONitor

displays the entry names as they are processed, for use when the input file is a wild-card entry name like SW:*_Ecoli.

REFERENCES

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.

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.

Printed: April 22, 1996 15:53 (1162)