EMBOSS: pepcoil

| pepcoil

## Wiki

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## Function

Predict coiled coil regions in protein sequences

## Description

pepcoil calculates the probability of a coiled-coil structure for windows of (by default) 28 residues through a protein sequence using the method of Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4. It reads one or more sequences and writes a standard EMBOSS report file including the location and score of the putative coiled-coil structures and their score for each input sequence. Optionally, coiled coil regions, non-coiled coil regions and coil frameshifts are reported.

## Usage

Here is a sample session with pepcoil

    % pepcoil
    Predict coiled coil regions in protein sequences
    Input protein sequence(s): tsw:gcn4_yeast
    Window size [28]:
    Output report [gcn4_yeast.pepcoil]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Predict coiled coil regions in protein sequences
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Protein sequence(s) filename and optional
                                      format, or reference (input USA)
       -window             integer    [28] Window size (Integer from 7 to 28)
      [-outfile]           report     [*.pepcoil] Output report file name (default
                                      -rformat motif)

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -[no]coil           boolean    [Y] Report coiled coil regions
       -frame              boolean    [Yes if -coil is true] Show coil frameshifts
       -other              boolean    [N] Report non coiled coil regions

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -scircular1         boolean    Sequence is circular
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -rformat2           string     Report format
       -rname2             string     Base file name
       -rextension2        string     File name extension
       -rdirectory2        string     Output directory
       -raccshow2          boolean    Show accession number in the report
       -rdesshow2          boolean    Show description in the report
       -rscoreshow2        boolean    Show the score in the report
       -rstrandshow2       boolean    Show the nucleotide strand in the report
       -rusashow2          boolean    Show the full USA in the report
       -rmaxall2           integer    Maximum total hits to report
       -rmaxseq2           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
-window | integer | Window size | Integer from 7 to 28 | 28
[-outfile] (Parameter 2) | report | Output report file name | (default -rformat motif) | <*>.pepcoil
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-[no]coil | boolean | Report coiled coil regions | Boolean value Yes/No | Yes
-frame | boolean | Show coil frameshifts | Boolean value Yes/No | Yes if -coil is true
-other | boolean | Report non coiled coil regions | Boolean value Yes/No | No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated report qualifiers
-rformat2 -rformat_outfile | string | Report format | Any string | motif
-rname2 -rname_outfile | string | Base file name | Any string |
-rextension2 -rextension_outfile | string | File name extension | Any string |
-rdirectory2 -rdirectory_outfile | string | Output directory | Any string |
-raccshow2 -raccshow_outfile | boolean | Show accession number in the report | Boolean value Yes/No | N
-rdesshow2 -rdesshow_outfile | boolean | Show description in the report | Boolean value Yes/No | N
-rscoreshow2 -rscoreshow_outfile | boolean | Show the score in the report | Boolean value Yes/No | Y
-rstrandshow2 -rstrandshow_outfile | boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y
-rusashow2 -rusashow_outfile | boolean | Show the full USA in the report | Boolean value Yes/No | N
-rmaxall2 -rmaxall_outfile | integer | Maximum total hits to report | Any integer value | 0
-rmaxseq2 -rmaxseq_outfile | integer | Maximum hits to report for one sequence | Any integer value | 0
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

pepcoil reads one or more protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### Input files for usage example

'tsw:gcn4_yeast' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:gcn4_yeast

    ID   GCN4_YEAST              Reviewed;         281 AA.
    AC   P03069; D3DLN9; P03068; Q70D88; Q70D91; Q70D96; Q70D99; Q70DA0;
    AC   Q96UT3;
    DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
    DT   21-JUL-1986, sequence version 1.
    DT   13-JUN-2012, entry version 139.
    DE   RecName: Full=General control protein GCN4;
    DE   AltName: Full=Amino acid biosynthesis regulatory protein;
    GN   Name=GCN4; Synonyms=AAS3, ARG9; OrderedLocusNames=YEL009C;
    OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
    OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
    OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
    OX   NCBI_TaxID=559292;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=85038531; PubMed=6387704; DOI=10.1073/pnas.81.20.6442;
    RA   Hinnebusch A.G.;
    RT   "Evidence for translational regulation of the activator of general
    RT   amino acid control in yeast.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:6442-6446(1984).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=84298088; PubMed=6433345; DOI=10.1073/pnas.81.16.5096;
    RA   Thireos G., Penn M.D., Greer H.;
    RT   "5' untranslated sequences are required for the translational control
    RT   of a yeast regulatory gene.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 81:5096-5100(1984).
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS PRO-24; SER-62;
    RP   ALA-82; ALA-91; ALA-125 AND GLU-196.
    RC   STRAIN=CLIB 219, CLIB 382, CLIB 388, CLIB 410, CLIB 413, CLIB 556,
    RC   CLIB 630, CLIB 95, K1, R12, R13, Sigma 1278B, YIIc12, and YIIc17;
    RX   PubMed=15087486; DOI=10.1093/nar/gkh529;
    RA   Leh-Louis V., Wirth B., Despons L., Wain-Hobson S., Potier S.,
    RA   Souciet J.-L.;
    RT   "Differential evolution of the Saccharomyces cerevisiae DUP240
    RT   paralogs and implication of recombination in phylogeny.";
    RL   Nucleic Acids Res. 32:2069-2078(2004).
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    RC   STRAIN=ATCC 204511 / S288c / AB972;
    RX   MEDLINE=97313264; PubMed=9169868;
    RA   Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
    RA   Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
    RA   Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G.,
    RA   Hunicke-Smith S., Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H.,
    RA   Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P.,
    RA   Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T.,
    RA   Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.;
    RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";

      [Part of this file has been deleted for brevity]

    FT                                /FTId=PRO_0000076490.
    FT   DOMAIN      253    274       Leucine-zipper.
    FT   DNA_BIND    231    249       Basic motif.
    FT   REGION       89    100       Required for transcriptional activation.
    FT   REGION      106    125       Required for transcriptional activation.
    FT   MOD_RES      17     17       Phosphoserine.
    FT   MOD_RES     165    165       Phosphothreonine; by PHO85.
    FT   MOD_RES     218    218       Phosphoserine.
    FT   VARIANT      24     24       S -> P (in strain: CLIB 219).
    FT   VARIANT      62     62       P -> S (in strain: CLIB 630 haplotype
    FT                                Ha2).
    FT   VARIANT      82     82       T -> A (in strain: CLIB 556 haplotype
    FT                                Ha1).
    FT   VARIANT      91     91       D -> A (in strain: CLIB 95, CLIB 219,
    FT                                CLIB 382, CLIB 388, CLIB 410, CLIB 413,
    FT                                CLIB 556, CLIB 630, K1, R12, R13
    FT                                haplotype Ha2, Sigma 1278B haplotype Ha1,
    FT                                YIIc12 and YIIc17).
    FT   VARIANT     125    125       D -> A (in strain: CLIB 556 haplotype
    FT                                Ha1).
    FT   VARIANT     196    196       D -> E (in strain: CLIB 388, CLIB 410,
    FT                                CLIB 413, CLIB 630 haplotype Ha1, K1,
    FT                                YIIc12 haplotype Ha2 and YIIc17 haplotype
    FT                                Ha1).
    FT   MUTAGEN      97     98       FF->AA: Reduces transcriptional
    FT                                activation activity; when associated with
    FT                                A-107; A-110; A-113; A-120; A-123 and A-
    FT                                124.
    FT   MUTAGEN     107    107       M->A: Reduces transcriptional activation
    FT                                activity; when associated with A-97; A-
    FT                                98; A-110; A-113; A-120; A-123 and A-124.
    FT   MUTAGEN     110    110       Y->A: Reduces transcriptional activation
    FT                                activity; when associated with A-97; A-
    FT                                98; A-107; A-113; A-120; A-123 and A-124.
    FT   MUTAGEN     113    113       L->A: Reduces transcriptional activation
    FT                                activity; when associated with A-97; A-
    FT                                98; A-107; A-110; A-120; A-123 and A-124.
    FT   MUTAGEN     120    124       WTSLF->ATSAA: Reduces transcriptional
    FT                                activation activity; when associated with
    FT                                A-97; A-98; A-107; A-110 and A-113.
    FT   CONFLICT    239    281       ARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG
    FT                                ER -> PGVLVRESCKE (in Ref. 2; AAA65521).
    FT   HELIX       230    248
    FT   HELIX       251    280
    SQ   SEQUENCE   281 AA;  31310 MW;  2ED1B8E35D509578 CRC64;
         MSEYQPSLFA LNPMGFSPLD GSKSTNENVS ASTSTAKPMV GQLIFDKFIK TEEDPIIKQD
         TPSNLDFDFA LPQTATAPDA KTVLPIPELD DAVVESFFSS STDSTPMFEY ENLEDNSKEW
         TSLFDNDIPV TTDDVSLADK AIESTEEVSL VPSNLEVSTT SFLPTPVLED AKLTQTRKVK
         KPNSVVKKSH HVGKDDESRL DHLGVVAYNR KQRSIPLSPI VPESSDPAAL KRARNTEAAR
         RSRARKLQRM KQLEDKVEEL LSKNYHLENE VARLKKLVGE R
    //

## 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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default the report is in 'motif' format.

### Output files for usage example

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.

### File: gcn4_yeast.pepcoil

    ########################################
    # Program: pepcoil
    # Rundate: Sun 15 Jul 2012 12:00:00
    # Commandline: pepcoil
    #    -sequence tsw:gcn4_yeast
    # Report_format: motif
    # Report_file: gcn4_yeast.pepcoil
    ########################################

    #=======================================
    #
    # Sequence: GCN4_YEAST     from: 1   to: 281
    # HitCount: 1
    #
    # Window size: 28 residues
    #
    #=======================================

    Max_coil_pos at "*"

    (1) Score 1.910 length 49 at residues 233->281
                               *
     Sequence: ARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER
               |                                               |
             233                                               281
     Probability: 1.000
     Predict: coiled
     Max_coil_pos: 249

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

## Data files

None.

## Notes

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.

## 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
--- | ---
garnier | Predict protein secondary structure using GOR method
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
pepnet | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence

## Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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

None