pepwindow Function   --> Displays protein hydropathyDescription   pepwindow reads in a protein sequence and displays a graph of the   classic Kyte & Doolittle hydropathy plot of that protein.Usage   Here is a sample session with pepwindow% pepwindow tsw:hba_human Displays protein hydropathyGraph type [x11]: cpsCreated pepwindow.ps   Go to the input files for this example   Go to the output files for this exampleCommand 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)   Additional (Optional) qualifiers:   -datafile           datafile   [Enakai.dat] AAINDEX entry data file   -length             integer    [7] Window size (Integer from 1 to 200)   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   -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 messagesInput file format   pepwindow reads any protein sequence USA.  Input files for usage example   'tsw:hba_human' is a sequence entry in the example protein database   'tsw'  Database entry: tsw:hba_humanID   HBA_HUMAN      STANDARD;      PRT;   141 AA.AC   P01922;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 ALPHA CHAIN.GN   HBA1 AND HBA2.OS   Homo sapiens (Human), Pan troglodytes (Chimpanzee), andOS   Pan paniscus (Pygmy chimpanzee) (Bonobo).OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.RN   [1]RP   SEQUENCE FROM N.A. (ALPHA-1).RX   MEDLINE; 81088339.RA   MICHELSON A.M., ORKIN S.H.;RT   "The 3' untranslated regions of the duplicated human alpha-globinRT   genes are unexpectedly divergent.";RL   Cell 22:371-377(1980).RN   [2]RP   SEQUENCE FROM N.A. (ALPHA-2).RX   MEDLINE; 81175088.RA   LIEBHABER S.A., GOOSSENS M.J., KAN Y.W.;RT   "Cloning and complete nucleotide sequence of human 5'-alpha-globinRT   gene.";RL   Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).RN   [3]RP   SEQUENCE FROM N.A. (ALPHA-2).RX   MEDLINE; 80137531.RA   WILSON J.T., WILSON L.B., REDDY V.B., CAVALLESCO C., GHOSH P.K.,RA   DERIEL J.K., FORGET B.G., WEISSMAN S.M.;RT   "Nucleotide sequence of the coding portion of human alpha globinRT   messenger RNA.";RL   J. Biol. Chem. 255:2807-2815(1980).RN   [4]RP   SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).RA   FLINT J., HIGGS D.R.;RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.RN   [5]RP   SEQUENCE.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   [6]RP   SEQUENCE.RA   HILL R.J., KONIGSBERG W.;RT   "The structure of human hemoglobin: IV. The chymotryptic digestion ofRT   the alpha chain of human hemoglobin.";RL   J. Biol. Chem. 237:3151-3156(1962).RN   [7]  [Part of this file has been deleted for brevity]FT                                /FTId=VAR_002841.FT   VARIANT     130    130       A -> D (IN YUDA; O2 AFFINITY DOWN).FT                                /FTId=VAR_002842.FT   VARIANT     131    131       S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE;FT                                CAUSES ALPHA-THALASSEMIA).FT                                /FTId=VAR_002843.FT   VARIANT     133    133       S -> R (IN VAL DE MARNE; O2 AFFINITY UP).FT                                /FTId=VAR_002844.FT   VARIANT     135    135       V -> E (IN PAVIE).FT                                /FTId=VAR_002845.FT   VARIANT     136    136       L -> M (IN CHICAGO).FT                                /FTId=VAR_002846.FT   VARIANT     136    136       L -> P (IN BIBBA; UNSTABLE;FT                                CAUSES ALPHA-THALASSEMIA).FT                                /FTId=VAR_002847.FT   VARIANT     138    138       S -> P (IN ATTLEBORO; O2 AFFINITY UP).FT                                /FTId=VAR_002848.FT   VARIANT     139    139       K -> E (IN HANAKAMI; O2 AFFINITY UP).FT                                /FTId=VAR_002849.FT   VARIANT     139    139       K -> T (IN TOKONAME; O2 AFFINITY UP).FT                                /FTId=VAR_002850.FT   VARIANT     140    140       Y -> H (IN ROUEN; O2 AFFINITY UP).FT                                /FTId=VAR_002851.FT   VARIANT     141    141       R -> C (IN NUNOBIKI; O2 AFFINITY UP).FT                                /FTId=VAR_002852.FT   VARIANT     141    141       R -> L (IN LEGNANO; O2 AFFINITY UP).FT                                /FTId=VAR_002853.FT   VARIANT     141    141       R -> H (IN SURESNES; O2 AFFINITY UP).FT                                /FTId=VAR_002854.FT   VARIANT     141    141       R -> P (IN SINGAPORE).FT                                /FTId=VAR_002855.FT   HELIX         4     35FT   HELIX        37     42FT   TURN         44     45FT   TURN         50     51FT   HELIX        53     71FT   TURN         72     74FT   HELIX        76     79FT   TURN         80     80FT   HELIX        81     89FT   TURN         90     91FT   TURN         95     95FT   HELIX        96    112FT   TURN        114    116FT   HELIX       119    136FT   TURN        137    139SQ   SEQUENCE   141 AA;  15126 MW;  5EC7DB1E CRC32;     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA     VHASLDKFLA SVSTVLTSKY R//Output file format   An image is displayed on the specified graphics device.  Output files for usage example  Graphics File: pepwindow.ps   [pepwindow results]Data files   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   pepwindow reads the Kyte-Doolittle hydropathy data from the file   'Enakai.dat'   The EMBOSS data file 'Enakai.dat' contains :-D Hydropathy index (Kyte-Doolittle, 1982)R 0807099A Kyte, J. and Doolittle, R.F.T A simple method for displaying the hydropathic character of a proteinJ J. Mol. Biol. 157, 105-132 (1982)C CHOC760103    0.964  JANJ780102    0.922  DESM900102    0.898  EISD860103    0.897  CHOC760104    0.889  WOLR810101    0.885  RADA880101    0.884  MANP780101    0.881  EISD840101    0.878  PONP800103    0.870  NAKH920108    0.868  JANJ790101    0.867  JANJ790102    0.866  PONP800102    0.861  MEIH800103    0.856  PONP800101    0.851  PONP800108    0.850  WARP780101    0.845  RADA880108    0.842  ROSG850102    0.841  DESM900101    0.837  BIOV880101    0.829  RADA880107    0.828  LIFS790102    0.824  KANM800104    0.824  CIDH920104    0.824  MIYS850101    0.821  RADA880104    0.819  NAKH900111    0.817  NISK800101    0.812  FAUJ830101    0.811  ARGP820103    0.806  NAKH920105    0.803  ARGP820102    0.803  KRIW790101   -0.805  CHOC760102   -0.838  GUYH850101   -0.843  RACS770102   -0.844  JANJ780103   -0.845  ROSM880101   -0.845  PRAM900101   -0.850  JANJ780101   -0.852  GRAR740102   -0.859  MEIH800102   -0.871  ROSM880102   -0.878  OOBM770101   -0.899I   A/L    R/K    N/M    D/F    C/P    Q/S    E/T    G/W    H/Y    I/V    1.8   -4.5   -3.5   -3.5    2.5   -3.5   -3.5   -0.4   -3.2    4.5    3.8   -3.9    1.9    2.8   -1.6   -0.8   -0.7   -0.9   -1.3    4.2//   pepwindow can use any of the "Nakai et al." database of amino acid   parameters - these used to be in a database called "NAKAI" but are now   in one called "AAINDEX". EMBOSS has a program aaindexextract that   takes data from this database and makes it available for pepwindow.   1. FTP the AAINDEX database from Japan:   ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1   2. Run aaindexextract with the aaindex1 file as input (or ask whoever   installs EMBOSS to run it)   3. Run pepwindow with -datafile specifying the name of whatever   "AAINDEX" datafile you wish to use. (Use embossdata -showall to see   your available "AAINDEX" data file names.)Notes   None.ReferencesKyte, J. and Doolittle, R.F.A simple method for displaying the hydropathic character of a proteinJ. Mol. Biol. 157, 105-132 (1982)Warnings   None.Diagnostic Error Messages   None.Exit status   0 upon successful completion.Known bugs   None.See also   Program name                         Description   backtranambig Back translate a protein sequence to ambiguous codons   backtranseq   Back translate a protein sequence   charge        Protein charge plot   checktrans    Reports STOP codons and ORF statistics of a protein   compseq       Count 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   pepinfo       Plots simple amino acid properties in parallel   pepstats      Protein statistics   pepwindowall  Displays protein hydropathy of a set of sequences   pepwindow can use any of the "Nakai et al." database of amino acid   parameters - these are in a database called "AAINDEX". The program   aaindexextract takes data from this database and makes it available   for pepwindow.Author(s)   Ian Longden (il