
                                  pepinfo 



Function

   Plots simple amino acid properties in parallel

Description

   pepinfo detects and displays various useful metrics about a protein
   sequence.

   It can plot and display the following properties:
     * plots of hydrophobicity (using the method of Kyte & Doolittle), of
       OHM (Sweet & Eisenberg), or of consensus parameters (Eisenberg et
       al))
     * a histogram of the presence of residues with the physico-chemical
       properties: Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar,
       Charged, Positive, Negative.

   The data are also written out to a data file.

Usage

   Here is a sample session with pepinfo


% pepinfo 
Plots simple amino acid properties in parallel
Input sequence: tsw:opsd_human
Graph type [x11]: cps
Output file [opsd_human.pepinfo]: 

Created pepinfo.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   Sequence USA
   -graph              xygraph    Graph type
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -aaproperties       datafile   Amino acid properties filename
   -aahydropathy       datafile   Hydropathy data filename
   -hwindow            integer    Window size for hydropathy averaging

   Advanced (Unprompted) qualifiers:
   -[no]generalplot    boolean    Plot histogram of general properties
   -[no]hydropathyplot boolean    Plot graphs of hydropathy

   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
   -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

   "-outfile" associated qualifiers
   -odirectory2         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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png, xml EMBOSS_GRAPHICS value, or x11
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.pepinfo
   Additional (Optional) qualifiers Allowed values Default
   -aaproperties Amino acid properties filename Data file
   Eaa_properties.dat
   -aahydropathy Hydropathy data filename Data file Eaa_hydropathy.dat
   -hwindow Window size for hydropathy averaging Integer 1 or more 9
   Advanced (Unprompted) qualifiers Allowed values Default
   -[no]generalplot Plot histogram of general properties Boolean value
   Yes/No Yes
   -[no]hydropathyplot Plot graphs of hydropathy Boolean value Yes/No Yes

Input file format

   pepinfo reads a protein sequence USA.

  Input files for usage example

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

  Database entry: tsw:opsd_human

ID   OPSD_HUMAN     STANDARD;      PRT;   348 AA.
AC   P08100; Q16414;
DT   01-AUG-1988 (Rel. 08, Created)
DT   01-AUG-1988 (Rel. 08, Last sequence update)
DT   15-JUL-1999 (Rel. 38, Last annotation update)
DE   RHODOPSIN.
GN   RHO.
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 84272729.
RA   NATHANS J., HOGNESS D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   SEQUENCE OF 1-120 FROM N.A.
RA   BENNETT J., BELLER B., SUN D., KARIKO K.;
RL   Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   REVIEW ON ADRP VARIANTS.
RX   MEDLINE; 94004905.
RA   AL-MAGHTHEH M., GREGORY C., INGLEHEARN C., HARDCASTLE A.,
RA   BHATTACHARYA S.;
RT   "Rhodopsin mutations in autosomal dominant retinitis pigmentosa.";
RL   Hum. Mutat. 2:249-255(1993).
RN   [4]
RP   VARIANT ADRP HIS-23.
RX   MEDLINE; 90136922.
RA   DRYJA T.P., MCGEE T.L., REICHEI E., HAHN L.B., COWLEY G.S.,
RA   YANDELL D.W., SANDBERG M.A., BERSON E.L.;
RT   "A point mutation of the rhodopsin gene in one form of retinitis
RT   pigmentosa.";
RL   Nature 343:364-366(1990).
RN   [5]
RP   VARIANTS ADRP.
RX   MEDLINE; 91051574.
RA   FARRAR G.J., KENNA P., REDMOND R., MCWILLIAM P., BRADLEY D.G.,
RA   HUMPHRIES M.M., SHARP E.M., INGLEHEARN C.F., BASHIR R., JAY M.,
RA   WATTY A., LUDWIG M., SCHINZEL A., SAMANNS C., GAL A.,
RA   BHATTACHARYA S.S., HUMPHRIES P.;
RT   "Autosomal dominant retinitis pigmentosa: absence of the rhodopsin
RT   proline-->histidine substitution (codon 23) in pedigrees from
RT   Europe.";
RL   Am. J. Hum. Genet. 47:941-945(1990).
RN   [6]
RP   VARIANTS ADRP HIS-23; ARG-58; LEU-347 AND SER-347.
RX   MEDLINE; 91015273.


  [Part of this file has been deleted for brevity]

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -> M (EFFECT NOT KNOWN).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -> P (IN ADRP).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (IN ADRP).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (IN ADRP).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (IN ADRP).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (IN ADRP).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       MISSING (IN ADRP).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       MISSING (IN ADRP).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (IN ADRP).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (IN ADRP).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (IN CSNB4).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (IN ADRP).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (IN ADRP).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (IN ADRP).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (IN ADRP).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (IN ADRP).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (IN ADRP).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (IN ADRP; COMMON VARIANT).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (IN ADRP).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (IN ADRP).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (IN ADRP).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38892 MW;  07443BEA CRC32;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//

Output file format

   Graphs are written to the selected graphics device.

  Output files for usage example

  File: opsd_human.pepinfo

Printing out Tiny residues in OPSD_HUMAN from position 1 to 348

Position  Residue                       Result
       1       M                               0
       2       N                               0
       3       G                               1
       4       T                               1
       5       E                               0
       6       G                               1
       7       P                               0
       8       N                               0
       9       F                               0
      10       Y                               0
      11       V                               0
      12       P                               0
      13       F                               0
      14       S                               1
      15       N                               0
      16       A                               1
      17       T                               1
      18       G                               1
      19       V                               0
      20       V                               0
      21       R                               0
      22       S                               1
      23       P                               0
      24       F                               0
      25       E                               0
      26       Y                               0
      27       P                               0
      28       Q                               0
      29       Y                               0
      30       Y                               0
      31       L                               0
      32       A                               1
      33       E                               0
      34       P                               0
      35       W                               0
      36       Q                               0
      37       F                               0
      38       S                               1
      39       M                               0
      40       L                               0
      41       A                               1
      42       A                               1
      43       Y                               0
      44       M                               0
      45       F                               0
      46       L                               0
      47       L                               0


  [Part of this file has been deleted for brevity]

  301       Y                           0.500
  302       N                           0.549
  303       P                           0.633
  304       V                           0.636
  305       I                           0.553
  306       Y                           0.438
  307       I                           0.358
  308       M                           0.250
  309       M                           0.262
  310       N                          -0.172
  311       K                          -0.288
  312       Q                          -0.409
  313       F                          -0.409
  314       R                          -0.362
  315       N                          -0.281
  316       C                          -0.120
  317       M                           0.128
  318       L                           0.028
  319       T                           0.341
  320       T                           0.481
  321       I                           0.282
  322       C                           0.124
  323       C                           0.020
  324       G                           0.143
  325       K                           0.202
  326       N                          -0.051
  327       P                          -0.183
  328       L                          -0.298
  329       G                          -0.282
  330       D                          -0.136
  331       D                           0.020
  332       E                           0.001
  333       A                           0.003
  334       S                          -0.070
  335       A                          -0.137
  336       T                          -0.042
  337       V                          -0.042
  338       S                          -0.117
  339       K                          -0.117
  340       T                          -0.280
  341       E                          -0.154
  342       T                          -0.206
  343       S                          -0.172
  344       Q                           0.063
  345       V                           0.000
  346       A                           0.000
  347       P                           0.000
  348       A                           0.000



  Graphics File: pepinfo.ps

   [pepinfo results]

   The output file 'pepinfo.out' contains the coordinates from the
   graphs.

   For the first set of graphs, 9 sets of true/false values are written
   out. For the second set of graphs, 3 sets of hydrophobicity values are
   written.

Data files

   The physico-chemical properties of the residues are read from the
   EMBOSS data file 'Eaa_properties.dat'. This file can be copied into
   your current directory and inspected ot altered by using the
   application 'embossdata -fetch'. Another file can be specified using
   the qualifier '-aaproperties'.

   The hydropathy data of the residues are read from the EMBOSS data file
   'Eaa_hydropathy.dat'. This file can be copied into your current
   directory and inspected ot altered by using the application
   'embossdata -fetch'. Another file can be specified using the qualifier
   '-aahydropathy'.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by EMBOSS
   environment variable EMBOSS_DATA.

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   None.

References

    1. Kyte J, Doolittle RF A simple method for displaying the
       hydropathic character of a protein. J Mol Biol 1982 May
       5;157(1):105-132
    2. Sweet RM, Eisenberg D Correlation of sequence hydrophobicities
       measures similarity in three-dimensional protein structure. J Mol
       Biol 1983 Dec 25;171(4):479-488
    3. Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic
       moment: a measure of the amphiphilicity of a helix. Nature 1982
       Sep 23;299(5881):371-4

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                          Description
   backtranseq  Back translate a protein sequence
   charge       Protein charge plot
   checktrans   Reports STOP codons and ORF statistics of a protein
   compseq      Counts the composition of dimer/trimer/etc words in a sequence
   emowse       Protein identification by mass spectrometry
   freak        Residue/base frequency table or plot
   iep          Calculates the isoelectric point of a protein
   mwcontam     Shows molwts that match across a set of files
   mwfilter     Filter noisy molwts from mass spec output
   octanol      Displays protein hydropathy
   pepstats     Protein statistics
   pepwindow    Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences

Author(s)

   Mark Faller (current e-mail address unknown)
   while he was with:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Written (1999) - Mark Faller

Target users

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

Comments

   None
