pepwheel.txt

emboss的linux版本的源代码

                                 pepwheel 



Function

   Shows protein sequences as helices

Description

   pepwheel displays peptide sequences in a helical representation.

   This gives a view of a helix from a protein sequence looking down the
   axis of the helix.

   It is useful for highlighting amphipathicity and other properties of
   residues around a helix.

Usage

   Here is a sample session with pepwheel


% pepwheel tsw:hbb_human -send 30 
Shows protein sequences as helices
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

   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,
                                  tekt, tek, none, data, xterm, png)

   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 is
                                  accepted)
*  -diamonds           string     [DENQST] By default the residues DENQST are
                                  marked with diamonds. (Any string is
                                  accepted)
*  -octags             string     [HKR] By default the positively charged
                                  residues HKR are marked with octagons. (Any
                                  string is accepted)

   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
   -sformat1           string     Input sequence format
   -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 standard output
   -filter             boolean    Read standard input, write 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. 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

Input file format

   pepwheel reads any protein sequence USA.

  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      STANDARD;      PRT;   146 AA.
AC   P02023;
DT   21-JUL-1986 (Rel. 01, Created)
DT   21-JUL-1986 (Rel. 01, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   HEMOGLOBIN BETA CHAIN.
GN   HBB.
OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS   Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE.
RC   SPECIES=HUMAN;
RA   BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA   RUDLOFF V., WITTMANN-LIEBOLD B.;
RT   "The constitution of normal adult human haemoglobin.";
RL   Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 81064667.
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   SEQUENCE OF 121-146 FROM N.A.
RC   SPECIES=HUMAN;
RX   MEDLINE; 85205333.
RA   LANG K.M., SPRITZ R.A.;
RT   "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT   segments.";
RL   Gene 33:191-196(1985).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC   SPECIES=HUMAN;
RX   MEDLINE; 76027820.
RA   FERMI G.;
RT   "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT   2.5-A resolution: refinement of the atomic model.";
RL   J. Mol. Biol. 97:237-256(1975).
RN   [5]
RP   SEQUENCE.
RC   SPECIES=P.TROGLODYTES;
RX   MEDLINE; 66071496.
RA   RIFKIN D.B., KONIGSBERG W.;
RT   "The characterization of the tryptic peptides from the hemoglobin of
RT   the chimpanzee (Pan troglodytes).";
RL   Biochim. Biophys. Acta 104:457-461(1965).
RN   [6]


  [Part of this file has been deleted for brevity]

FT   VARIANT     140    140       A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT                                /FTId=VAR_003081.
FT   VARIANT     140    140       A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT                                O2 AFFINITY UP).
FT                                /FTId=VAR_003082.
FT   VARIANT     141    141       L -> R (IN OLMSTED; UNSTABLE).
FT                                /FTId=VAR_003083.
FT   VARIANT     142    142       A -> D (IN OHIO; O2 AFFINITY UP).
FT                                /FTId=VAR_003084.
FT   VARIANT     143    143       H -> D (IN RANCHO MIRAGE).
FT                                /FTId=VAR_003085.
FT   VARIANT     143    143       H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT                                /FTId=VAR_003086.
FT   VARIANT     143    143       H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT                                /FTId=VAR_003087.
FT   VARIANT     143    143       H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT                                /FTId=VAR_003088.
FT   VARIANT     144    144       K -> E (IN MITO; O2 AFFINITY UP).
FT                                /FTId=VAR_003089.
FT   VARIANT     145    145       Y -> C (IN RAINIER; O2 AFFINITY UP).
FT                                /FTId=VAR_003090.
FT   VARIANT     145    145       Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT                                /FTId=VAR_003091.
FT   VARIANT     146    146       H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT                                /FTId=VAR_003092.
FT   VARIANT     146    146       H -> L (IN COWTOWN; O2 AFFINITY UP).
FT                                /FTId=VAR_003093.
FT   VARIANT     146    146       H -> P (IN YORK; O2 AFFINITY UP).
FT                                /FTId=VAR_003094.
FT   VARIANT     146    146       H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT                                /FTId=VAR_003095.
FT   HELIX         5     15
FT   TURN         16     17
FT   HELIX        20     34
FT   HELIX        36     41
FT   HELIX        43     45
FT   HELIX        51     55
FT   TURN         56     56
FT   HELIX        58     75
FT   TURN         76     77
FT   HELIX        78     94
FT   TURN         95     96
FT   TURN        100    100
FT   HELIX       101    121
FT   HELIX       124    142
FT   TURN        143    144
SQ   SEQUENCE   146 AA;  15867 MW;  EC9744C9 CRC32;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
//

Output file format

   An image is output to the specified graphics device.

  Output files for usage example

  Graphics File: pepwheel.ps

   [pepwheel results]

Data files

   None.

Notes

   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.

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        Reads ABI file and display the trace
   cirdna         Draws circular maps of DNA constructs
   garnier        Predicts protein secondary structure
   helixturnhelix Report nucleic acid binding motifs
   hmoment        Hydrophobic moment calculation
   lindna         Draws linear maps of DNA constructs
   pepcoil        Predicts coiled coil regions
   pepnet         Displays proteins as a helical net
   prettyplot     Displays aligned sequences, with colouring and boxing
   prettyseq      Output sequence with translated ranges
   remap          Display sequence with restriction sites, translation etc
   seealso        Finds programs sharing group names
   showalign      Displays a multiple sequence alignment
   showdb         Displays information on the currently available databases
   showfeat       Show features of a sequence
   showseq        Display a sequence with features, translation etc
   sixpack        Display a DNA sequence with 6-frame translation and ORFs
   textsearch     Search sequence documentation. Slow, use SRS and Entrez!
   tmap           Displays membrane spanning regions

Author(s)

   Alan Bleasby (ajb