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pepwheel
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Draw a helical wheel diagram for a protein sequence
Description
pepwheel draws a helical wheel diagram for a protein sequence. This
displays the sequence in a helical representation as if looking down
the axis of the helix. It is useful for highlighting amphipathicity and
other properties of residues around a helix. By default, aliphatic
residues are marked with squares, hydrophilic residues are marked with
diamonds, and positively charged residues with octagons, although this
can be changed.
Usage
Here is a sample session with pepwheel
% pepwheel tsw:hbb_human -send 30
Draw a helical wheel diagram for a protein sequence
Graph type [x11]: cps
Created pepwheel.ps
Go to the input files for this example
Go to the output files for this example
Command line arguments
Draw a helical wheel diagram for a protein sequence
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Protein sequence filename and optional
format, or reference (input USA)
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers (* if not always prompted):
-steps integer [18] The number of residues plotted per turn
is this value divided by the 'turns' value.
(Integer from 2 to 100)
-turns integer [5] The number of residues plotted per turn
is the 'steps' value divided by this value.
(Integer from 1 to 100)
* -squares string [ILVM] By default the aliphatic residues
ILVM are marked with squares. (Any string)
* -diamonds string [DENQST] By default the residues DENQST are
marked with diamonds. (Any string)
* -octags string [HKR] By default the positively charged
residues HKR are marked with octagons. (Any
string)
Advanced (Unprompted) qualifiers:
-[no]wheel boolean [Y] Plot the wheel
-amphipathic toggle If this is true then the residues ACFGILMVWY
are marked as squares and all other
residues are unmarked. This overrides any
other markup that you may have specified
using the qualifiers '-squares', '-diamonds'
and '-octags'.
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
-squick1 boolean Read id and sequence only
-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
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
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
Input file format
pepwheel reads a single protein sequence.
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:hbb_human' is a sequence entry in the example protein database
'tsw'
Database entry: tsw:hbb_human
ID HBB_HUMAN Reviewed; 147 AA.
AC P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 13-JUN-2012, entry version 108.
DE RecName: Full=Hemoglobin subunit beta;
DE AltName: Full=Beta-globin;
DE AltName: Full=Hemoglobin beta chain;
DE Contains:
DE RecName: Full=LVV-hemorphin-7;
GN Name=HBB;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=77126403; PubMed=1019344;
RA Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT "Nucleotide sequence analysis of coding and noncoding regions of human
RT beta-globin mRNA.";
RL Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT "The nucleotide sequence of the human beta-globin gene.";
RL Cell 21:647-651(1980).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX PubMed=16175509; DOI=10.1086/491748;
RA Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT "The beta-globin recombinational hotspot reduces the effects of strong
RT selection around HbC, a recently arisen mutation providing resistance
RT to malaria.";
RL Am. J. Hum. Genet. 77:637-642(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT "DNA sequence of the human beta-globin gene isolated from a healthy
RT Chinese.";
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT "Unexpected patterns of globin mutations in thalassemia patients from
RT north of Portugal.";
[Part of this file has been deleted for brevity]
FT VARIANT 141 141 A -> V (in Puttelange; polycythemia; O(2)
FT affinity up).
FT /FTId=VAR_003082.
FT VARIANT 142 142 L -> R (in Olmsted; unstable).
FT /FTId=VAR_003083.
FT VARIANT 143 143 A -> D (in Ohio; O(2) affinity up).
FT /FTId=VAR_003084.
FT VARIANT 144 144 H -> D (in Rancho Mirage).
FT /FTId=VAR_003085.
FT VARIANT 144 144 H -> P (in Syracuse; O(2) affinity up).
FT /FTId=VAR_003087.
FT VARIANT 144 144 H -> Q (in Little Rock; O(2) affinity
FT up).
FT /FTId=VAR_003086.
FT VARIANT 144 144 H -> R (in Abruzzo; O(2) affinity up).
FT /FTId=VAR_003088.
FT VARIANT 145 145 K -> E (in Mito; O(2) affinity up).
FT /FTId=VAR_003089.
FT VARIANT 146 146 Y -> C (in Rainier; O(2) affinity up).
FT /FTId=VAR_003090.
FT VARIANT 146 146 Y -> H (in Bethesda; O(2) affinity up).
FT /FTId=VAR_003091.
FT VARIANT 147 147 H -> D (in Hiroshima; O(2) affinity up).
FT /FTId=VAR_003092.
FT VARIANT 147 147 H -> L (in Cowtown; O(2) affinity up).
FT /FTId=VAR_003093.
FT VARIANT 147 147 H -> P (in York; O(2) affinity up).
FT /FTId=VAR_003094.
FT VARIANT 147 147 H -> Q (in Kodaira; O(2) affinity up).
FT /FTId=VAR_003095.
FT CONFLICT 26 26 Missing (in Ref. 15; ACD39349).
FT CONFLICT 42 42 F -> L (in Ref. 13; AAR96398).
FT HELIX 6 16
FT TURN 21 23
FT HELIX 24 35
FT HELIX 37 42
FT HELIX 44 46
FT HELIX 52 57
FT HELIX 59 77
FT TURN 78 80
FT HELIX 82 94
FT TURN 95 97
FT HELIX 102 119
FT HELIX 120 122
FT HELIX 125 142
FT HELIX 144 146
SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64;
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
Output file format
The output is to the specified graphics device.
The results can be output in one of several formats by using the
command-line qualifier -graph xxx, where 'xxx' is replaced by the name
of the required device. Support depends on the availability of
third-party software packages.
The device names that output to a file are: ps (postscript), cps
(colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
information on supported devices.
Output files for usage example
Graphics File: pepwheel.ps
[pepwheel results]
Data files
None.
Notes
The number of residues plotted per turn is the specified "steps" value
(-steps) divided by the specified "turns" value (-turns).
The default settings for turn (5) and steps (18) apply to alpha
helices. For other possible secondary structures, see the following
table:
helix phi psi omega res/turn transl. turns steps
alpha -57 -47 180 3.6 1.50 5 18
3-10 -49 -26 180 3.0 2.00 1 3
pi -57 -70 180 4.4 1.15 5 22
PP I -83 158 0 3.33 1.9 3 10
PP II -78 149 180 3.0 3.12 1 3
PG II -80 150 180 3.0 3.1 1 3
anti Beta -139 135 -178 2.0 3.4 4 9
para Beta -119 113 180 2.0 3.2 4 9
PP is polyproline
PG II is polyGlycine.
When you specify the number of turns and steps, be aware that you
should remove common factors from these two numbers. For example, if
you (for some improbable reason) wished to plot a wheel with 8 turns in
18 steps (2.25 residues per turn) you should remove the common factor
(i.e. 2) and specify 4 turns in 9 steps.
References
1. Rachamandran and Sasisekharan, Adv. Protein Chem. 23:283-437, 1968
2. IUPAC-IUB Commission on biochemical nomenclature, Biochemistry
9:3471-3479, 1970
Warnings
When you specify the number of turns and steps, be aware that you
should remove common factors from these two numbers. For example, if
you (for some improbable reason) wished to plot a wheel with 8 turns in
18 steps (2.25 residues per turn) you should remove the common factor
(i.e. 2) and specify 4 turns in 9 steps.
Diagnostic Error Messages
None.
Exit status
0 upon successful completion.
Known bugs
None.
See also
Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draw circular map of DNA constructs
garnier Predict protein secondary structure using GOR method
helixturnhelix Identify nucleic acid-binding motifs in protein
sequences
iep Calculate the isoelectric point of proteins
lindna Draw linear maps of DNA constructs
pepcoil Predict coiled coil regions in protein sequences
pepinfo Plot amino acid properties of a protein sequence in parallel
pepnet Draw a helical net for a protein sequence
plotorf Plot potential open reading frames in a nucleotide sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showfeat Display features of a sequence in pretty format
showpep Display protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
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 (c) emboss.open-bio.org) not to the original author.
History
Written (March 1999) - Alan Bleasby
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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