
                                  octanol 



Function

   Draw a White-Wimley protein hydropathy plot

Description

   octanol draws a hydropathy plot for an input protein sequence. This
   plots the free energy difference calculated for windows over the
   protein sequence, of the residues in water compared to two lipid
   environments: i. Octanol (equivalent to inside a lipid bilayer). ii.
   The interface of a synthetic lipid bilayer. Free energy differences
   are calculated for each position in a window of 19 residues by
   default, about the size of a membrane spanning alpha-helix. The energy
   values for each residue are summed to get two values for each window.
   By default, the value plotted is the free energy difference between
   the interface and octanol environments, which is the best indicator of
   the location of probable transmembrane regions. Command line options
   allow the display of the octanol and interface values, or hiding the
   difference values. The experimental free energy values for the
   water-interface and water-octanol transitions are read from a datafile
   (Ewhite-wimley.dat)

Usage

   Here is a sample session with octanol


% octanol 
Draw a White-Wimley protein hydropathy plot
Input protein sequence: tsw:opsd_human
Graph type [x11]: ps

Created octanol.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]             xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png, gif)

   Additional (Optional) qualifiers:
   -datafile           datafile   [Ewhite-wimley.dat] White-Wimley data file
   -width              integer    [19] Window size (Integer from 1 to 200)
   -octanolplot        boolean    [N] Display the octanol plot
   -interfaceplot      boolean    [N] Display the interface plot
   -[no]differenceplot boolean    [Y] Display the difference plot

   Advanced (Unprompted) qualifiers: (none)
   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
   -gprompt2           boolean    Graph prompting
   -gdesc2             string     Graph description
   -gtitle2            string     Graph title
   -gsubtitle2         string     Graph subtitle
   -gxtitle2           string     Graph x axis title
   -gytitle2           string     Graph y axis title
   -goutfile2          string     Output file for non interactive displays
   -gdirectory2        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. 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

   octanol reads any 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              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
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=84272729; PubMed=6589631;
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   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;


  [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 RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     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

   octanol draws a graph showing the free energy calcuated over a sliding
   window.

  Output files for usage example

  Graphics File: octanol.ps

   [octanol results]

   The line on the default plot is the difference between the interface
   and octanol free energy calculations. Command line options allow the
   display of the interface and octanol values, or hiding the difference
   values.

   In the example, the human opsin protein has 7 transmembrane regions:
   37-61, 74-98, 114-133, 153-176, 203-230, 253-276 and 285-309. Each is
   about 20 residues in length, which is also the gap between tick marks
   on the sequence axis. All have energetic preferences for being in the
   lipid (octanol) enviroment - shown as being above the zero line - or
   have at least no clear preference.

   Running octanol with all three plots:

% octanol -interface -octanol
Input sequence: tsw:opsd_human
   Graph type [x11]:

   gives a graph with the water-interface and water-octanol plots.

   For those regions where the diference plot is close to zero, both the
   other two plots are above the line, showing a preference for either
   the octanol or the interface membrane environments rather than water.

Data files

   File Ewhite-wimley.dat contains the experimental free energy values
   for the water-interface and water-octanol transitions.

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

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   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

   Protein sequences that form transmembrane regions are assumed to have
   a thermodynamic preference for a hydrophobic environment (inside the
   membrane lipid bilayer), rather than an aqueous environment in water.
   The free energy change for each amino acid residue between a lipid and
   a water environment can be measured experimentally, and the values for
   peptides can be shown to be additive (White and Wimley 1999).

   For each amino acid residue in the protein, the free energy difference
   of the residue in lipid and water environments is measured in two
   ways. The first is the free energy difference between the protein in
   water and the protein associated with the interface (glycerol group)
   of a POPC (palmitoyloleoylphosphocholine) bilayer. The second is the
   free energy difference of the protein in water and the protein in
   octanol, equivalent to the environment inside a lipid bilayer.

   Residues which can be buried inside a lipid bilayer must be in a
   region of the peptide where most residues show a free energy
   difference in favour of being in an octanol environment or at least
   being in the lipid/water interface region. White and Wimley (1999)
   showed that a sliding window of either free energy difference will
   indicate the location of probable transmembrane regions, but that the
   best indicator is the difference between the two values, which is the
   free energy difference between the interface and octanol environments.

References

    1. White S.H. and Wimley W.C. (1999) "Membrane protein folding and
       stability: physical principles" Ann. Rev.Biophys. Biomol. Struct.
       28:319-365.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name Description
   backtranambig Back-translate a protein sequence to ambiguous
   nucleotide sequence
   backtranseq Back-translate a protein sequence to a nucleotide sequence
   charge Draw a protein charge plot
   checktrans Reports STOP codons and ORF statistics of a protein
   compseq Calculate the composition of unique words in sequences
   emowse Search protein sequences by digest fragment molecular weight
   freak Generate residue/base frequency table or plot
   iep Calculate the isoelectric point of proteins
   mwcontam Find weights common to multiple molecular weights files
   mwfilter Filter noisy data from molecular weights file
   pepinfo Plot amino acid properties of a protein sequence in parallel
   pepstats Calculates statistics of protein properties
   pepwindow Draw a Kyte-Doolittle hydropathy plot for a protein sequence
   pepwindowall Draw Kyte-Doolittle hydropathy plot for a protein
   alignment
   wordcount Count and extract unique words in DNA sequence(s)

Author(s)

   Ian Longden (il © sanger.ac.uk)
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

History

Target users

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

Comments

   None
