pepwindowall Function   Displays protein hydropathy of a set of sequencesDescription   pepwindowall produces a set of superimposed Kyte & Doolittle   hydropathy plots from an aligned set of protein sequences.   The result is the same as running pepwindow on a set of proteins with   aligning gaps and superimposing the plots.   It is useful for visualising the average hydropathy and its   variability along the alignment.Usage   Here is a sample session with pepwindowall% pepwindowall globins.msf -gxtitle="Base Number" -gytitle="hydropathy" Displays protein hydropathy of a set of sequencesGraph type [x11]: cpsCreated pepwindowall.ps   Go to the input files for this example   Go to the output files for this exampleCommand line arguments   Standard (Mandatory) qualifiers: [-sequences] seqset File containing a   sequence alignment [-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: "-sequences" associated qualifiers -sbegin1   integer Start of each sequence to be used -send1 integer End of each   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 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   pepwindowall reads any protein sequence USA for one or more aligned   sequences.  Input files for usage example  File: globins.msf!!AA_MULTIPLE_ALIGNMENT 1.0  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43//           1                                               50HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQRHBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQRHBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLSHBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLGMYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLEGLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQELGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD           51                                             100HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSEHBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSEHBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDHBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDMYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQGLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN           101                                            150HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAHBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVAHBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSHBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSMYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRGLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSALGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA           151        164HBB_HUMAN  NALAHKYH~~~~~~HBB_HORSE  NALAHKYH~~~~~~HBA_HUMAN  TVLTSKYR~~~~~~HBA_HORSE  TVLTSKYR~~~~~~MYG_PHYCA  KDIAAKYKELGYQGGLB5_PETMA Y~~~~~~~~~~~~~LGB2_LUPLU IVIKKEMNDAA~~~Output file format   An image is displayed on the specified graphics device.  Output files for usage example  Graphics File: pepwindowall.ps   [pepwindowall results]Data files   pepwindow reads the Kyte-Doolittle hydropathy data from the file   'Enakai.dat'   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   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//Notes   None.References    1. Kyte, J. and Doolittle, R.F. A simple method for displaying the       hydropathic character of a protein J. 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   pepwindow     Displays protein hydropathyAuthor(s)   Ian Longden (il