
                              EMBOSS: pepcoil
     _________________________________________________________________
   
                                Program pepcoil
                                       
Function

   Predicts coiled coil regions
   
Description

   Coiled coils are formed by two or three alpha helices in parallel and
   in register that cross at an angle of approximately 20 degrees, are
   strongly amphipathic and display a pattern of hydrophilic and
   hydrophobic residues that is repeated every seven residues. The seven
   positions of the heptad repeat are designated a through g, a and d
   being generally hydrophobic, while the others are hydrophilic.
   
   The parallel two-stranded alpha-helical coiled coil is the most
   frequently encountered subunit-oligomerization motif in proteins.
   
   pepcoil calculates the probability of a coiled-coil structure for
   windows of 28 residues through a protein sequence using the method of
   Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4
   
Usage

   Here is a sample session with pepcoil.

% pepcoil
Input sequence: sw:gcn4_yeast
Window size [28]:
Output file [gcn4_yeast.pepcoil]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -window             integer    Window size
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -[no]coil           bool       Report coiled coil regions
   -frame              bool       Show coil frameshifts
   -[no]other          bool       Report non coiled coil regions

   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
   -window Window size Integer from 7 to 28 28
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.pepcoil
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -[no]coil Report coiled coil regions Yes/No Yes
   -frame Show coil frameshifts Yes/No Yes if -coil is true
   -[no]other Report non coiled coil regions Yes/No Yes
   
Input file format

   It reads in a protein sequence.
   
Output file format

   Here is the output file from the example run. The SwissProt annotation
   marks the true leucine zipper motif as from 253 to 274. The leucine
   zipper is a special case of a coiled-coil region.
     _________________________________________________________________
   
PEPCOIL of GCN4_YEAST
   using a window of 28 residues


Other structures from 1 to 232 (232 residues)
   Max score: 1.283 (probability 0.21)

Prediction starts at 233
Probable coiled-coil from 233 to 281 (49 residues)
   Max score: 1.910 (probability 1.00)
     _________________________________________________________________
   
Data files

   None.
   
Notes

   None.
   
References

    1. Lupas A, van Dyke M & Stock J; Predicting Coiled Coils from
       Protein Sequences. Science 252:1162-4 (1991)
       
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
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
   helixturnhelix Report nucleic acid binding motifs
   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
   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 "PEPCOIL" by Peter Rice (EGCG 1991)
   
History

   Written (1999) - Alan Bleasby
   
Target users

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