EMBOSS: pepcoil

| ## 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