prophecy Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Create frequency matrix or profile from a multiple alignment Description prophecy generates for an input sequence alignment a simple frequency matrix (for use by profit) or a position specific weighted profile using either the Gribskov (1) or Henikoff (2) method (for use by prophet). For constructing a simple frequency matrix, a residue substitution matrix, gap opening and gap extension penalty must be specified. Algorithm The Gribskov scoring scheme is based on a notion of distance between a sequence and an ancestral or generalized sequence. For Henikoff it is based on weights of the diversity observed at each position in the alignment, rather than on a sequence distance measure. Usage Here is a sample session with prophecy % prophecy Create frequency matrix or profile from a multiple alignment Input (aligned) sequence set: globins.msf Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: globins Enter threshold reporting percentage [75]: Output file [globins.prophecy]: Go to the input files for this example Go to the output files for this example Example 2 % prophecy Create frequency matrix or profile from a multiple alignment Input (aligned) sequence set: globins.msf Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: g Scoring matrix [Epprofile]: Enter a name for the profile [mymatrix]: globins Gap opening penalty [3.0]: Gap extension penalty [0.3]: Output file [globins.prophecy]: Go to the output files for this example Command line arguments Create frequency matrix or profile from a multiple alignment Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqset (Aligned) sequence set filename and optional format, or reference (input USA) -type menu [F] Select type (Values: F (Frequency); G (Gribskov); H (Henikoff)) * -datafile matrixf ['Epprofile' for Gribskov type, or EBLOSUM62] Scoring matrix -name string [mymatrix] Enter a name for the profile (Any string) * -threshold integer [75] Enter threshold reporting percentage (Integer from 1 to 100) * -open float [3.0] Gap opening penalty (Any numeric value) * -extension float [0.3] Gap extension penalty (Any numeric value) [-outfile] outfile [*.prophecy] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" 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 "-outfile" associated qualifiers -odirectory2 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 and exit. 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 -version boolean Report version number and exit Input file format prophecy reads a protein or a nucleic sequence alignment USA. 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 50 HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 51 100 HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 101 150 HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 151 164 HBB_HUMAN NALAHKYH~~~~~~ HBB_HORSE NALAHKYH~~~~~~ HBA_HUMAN TVLTSKYR~~~~~~ HBA_HORSE TVLTSKYR~~~~~~ MYG_PHYCA KDIAAKYKELGYQG GLB5_PETMA Y~~~~~~~~~~~~~ LGB2_LUPLU IVIKKEMNDAA~~~ Output file format The output is a profile file. Output files for usage example File: globins.prophecy # Pure Frequency Matrix # Columns are amino acid counts A->Z # Rows are alignment positions 1->n Simple Name globins Length 164 Maximum score 496 Thresh 75 Consensus PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDAS HGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASLDK ALAGVANVLAHKYHDAAYQG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 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1 0 0 0 0 0 0 3 0 1 0 0 0 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 4 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 2 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 4 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 1 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 2 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 3 0 0 0 1 0 0 2 0 0 0 0 0 0 0 0 2 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 [Part of this file has been deleted for brevity] 0 0 0 1 0 0 0 1 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 5 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 0 2 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0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 2 0 0 1 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Output files for usage example 2 File: globins.prophecy # Gribskov Protein Profile # Columns are amino acids A->Z # Last column is indel penalty # Rows are alignment positions 1->n Gribskov Name globins Matrix pprofile Length 164 Max_score 939.76 Threshold 75 Gap_open 3.00 Gap_extend 0.30 Consensus PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLS KGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDK FLASVATVLASKYRELGYQG 0.65 0.00 0.13 0.13 0.13 -0.78 0.39 0.26 -0.26 0.00 0.13 -0.39 -0.26 0.00 0.00 1 .95 0.39 0.39 0.52 0.39 0.00 0.13 -1.04 0.00 -1.04 0.00 0.87 0.87 0.00 0.00 0.26 -0.26 -0.26 0.78 -0.39 -0.39 1.95 0.00 -0.26 1.04 0.78 -0.39 0.00 -0.26 -0.39 -0.39 -0.13 0.26 0.00 1.43 -0.65 0.00 0.13 0.00 0.87 0.87 0.26 0.00 0.26 -0.26 -0.26 0.26 0.26 -0.39 1.43 0.00 -0.26 1.04 0.78 -0.39 0.00 0.13 -0.26 -0.39 -0.13 0.26 0.00 1.95 -1.04 0.00 -0.13 0.00 0.87 0.87 0.39 0.00 -0.65 1.95 1.30 -1.30 0.78 0.52 -0.26 0.00 0.39 -0.65 -0.52 0.78 0.00 0.13 0.78 0.00 0.26 0.26 0.00 -0.26 -1.43 0.00 -0.65 0.00 0.87 0.87 0.52 0.00 0.26 0.26 0.26 -0.39 0.52 -0.13 0.26 0.00 0.26 -0.13 0.00 0.26 0.00 0. 39 -0.13 -0.13 0.39 1.95 0.00 0.26 -0.78 0.00 -0.39 0.00 0.87 0.87 0.78 0.00 0.26 0.78 0.65 -0.78 1.95 -0.26 -0.39 0.00 -0.13 -0.65 -0.39 0.52 0.00 0.39 0.26 -0.39 0.78 0.52 0.00 0.26 -1.30 0.00 -0.78 0.00 0.87 0.87 0.52 0.00 0.78 0.26 0.26 -0.39 0.78 -0.26 -0.13 0.00 0.26 -0.52 -0.39 0.39 0.00 0.52 -0.13 0.13 1.95 0.39 0.00 -0.13 0.39 0.00 -0.52 0.00 0.87 0.87 0.55 0.00 0.55 -0.55 -0.55 0.55 0.55 -0.82 3.00 0.00 -0.55 2.18 1.64 -0.82 0.00 0.27 -0.55 -0.82 -0.27 0.55 0.00 4.09 -2.18 0.00 -0.27 0.00 0.87 0.87 2.54 0.00 -0.27 -0.32 -0.09 1.06 1.35 -1.08 2.94 0.00 -0.85 3.15 2.61 -0.61 0.00 0.59 -0.12 -1.69 0.14 0.98 0.00 4.23 -2.38 0.00 -0.51 0.00 0.87 0.87 2.24 0.00 0.53 1.51 1.51 -2.35 1.63 1.78 -0.94 0.00 0.87 -1.29 -0.95 1.36 0.00 3 .28 2.29 1.16 2.64 0.88 0.00 -0.34 -1.65 0.00 -2.09 0.00 0.87 0.87 0.06 0.00 -3.83 -0.43 1.03 3.60 -1.14 -0.17 2.69 0.00 -0.69 5.14 4.17 -0.77 0.00 -0.97 0.49 -1.49 -1.20 -0.09 0.00 2.69 0.29 0.00 0.40 0.00 0.87 0.87 2.34 0.00 1.92 1.60 1.46 -1.97 4.07 -0.88 -0.35 0.00 0.60 -1.75 -1.10 1.54 0.00 1.77 -0.09 -0.35 4.65 3.47 0.00 0.36 -1.65 0.00 -2.19 0.00 0.87 0.87 3.56 0.00 -0.56 3.08 4.01 -2.96 3.46 0.68 -0.86 0.00 0.61 -1.47 -0.86 1.65 0.00 2.44 1.93 -0.41 1.83 1.56 0.00 0.12 -4.91 0.00 -2.67 0.00 0.87 0.87 1.59 0.00 -2.04 0.74 1.64 -0.20 0.62 0.32 -1.14 0.00 0.81 -0.20 -0.97 0.92 0.00 -0.07 0.56 1.53 2.23 0.21 0.00 -1.30 -0.69 0.00 0.04 0.00 0.87 0.87 1.76 0.00 -2.66 3.90 5.45 -3.07 2.38 1.83 1.09 0.00 1.32 0.56 0.65 1.73 0.00 1.1 3 4.50 0.18 0.20 0.84 0.00 2.14 -6.12 0.00 -2.99 0.00 4.55 4.55 0.57 0.00 -4.51 -0.66 0.05 2.08 -1.71 -0.46 2.21 0.00 3.59 4.32 4.87 -0.05 0.00 -0.45 1.01 0.88 -0.55 0.51 0.00 2.34 1.59 0.00 -0.98 0.00 4.55 4.55 4.31 0.00 2.80 1.03 1.03 -1.77 3.52 -1.31 1.53 0.00 0.57 -0.34 -0.04 1.04 0.00 2 .50 -0.41 -0.72 5.34 3.75 0.00 2.41 -2.26 0.00 -2.19 0.00 4.55 4.55 4.74 0.00 -1.43 0.36 0.77 -0.38 0.92 -0.39 1.19 0.00 1.43 2.10 2.53 0.30 0.00 2. 40 1.19 -0.39 1.01 1.53 0.00 2.06 -1.98 0.00 -1.81 0.00 4.55 4.55 3.51 0.00 1.23 0.46 0.46 0.06 1.08 0.82 4.18 0.00 -0.60 2.47 1.80 0.02 0.00 1.32 0.41 -1.03 0.19 1.45 0.00 5.05 -4.42 0.00 -0.32 0.00 4.55 4.55 0.79 0.00 -2.10 2.78 1.91 -1.99 0.99 0.86 1.55 0.00 2.21 0.69 1.51 1.02 0.00 0.7 9 1.57 1.55 0.42 1.92 0.00 2.12 -1.78 0.00 -2.33 0.00 4.55 4.55 2.32 0.00 -1.29 -0.01 -0.01 -1.03 0.59 -0.49 -1.33 0.00 3.70 -0.87 -0.58 1.35 0. 00 0.73 0.30 3.20 4.44 0.86 0.00 -1.40 1.49 0.00 -1.00 0.00 4.55 4.55 5.00 0.00 0.17 0.46 0.82 -0.02 1.95 -0.97 1.80 0.00 0.01 1.97 1.98 0.43 0.00 1.7 0 0.09 -1.69 1.93 4.27 0.00 2.35 -2.37 0.00 -1.16 0.00 4.55 4.55 -2.55 0.00 -5.95 -2.39 -2.60 2.54 -3.01 0.83 -2.78 0.00 3.36 0.58 -1.46 2.63 0.0 0 -2.83 -0.44 6.18 2.03 -1.52 0.00 -3.89 5.08 0.00 3.02 0.00 4.55 4.55 3.64 0.00 0.44 2.21 1.97 -1.76 3.66 -0.75 3.33 0.00 -0.33 1.62 1.37 0.41 0.00 1. 42 0.65 -1.71 1.00 1.89 0.00 5.44 -6.44 0.00 -2.04 0.00 4.55 4.55 1.26 0.00 -3.44 3.35 4.37 -4.35 1.02 1.47 -1.45 0.00 6.61 -2.18 0.11 2.59 0.00 2 .55 3.18 3.52 1.71 1.58 0.00 -1.06 -2.90 0.00 -4.41 0.00 4.55 4.55 5.63 0.00 1.62 -0.17 0.07 -0.23 2.38 -1.35 3.78 0.00 -0.99 2.86 2.17 -0.53 0.00 1.71 -0.40 -2.30 0.92 1.85 0.00 5.48 -4.58 0.00 -0.57 0.00 4.55 4.55 3.69 0.00 0.50 3.58 2.62 -2.00 2.31 1.96 -0.88 0.00 0.61 -1.50 -1.43 4.77 0.00 0 .16 1.47 -1.17 1.34 1.22 0.00 -0.72 -2.56 0.00 0.36 0.00 4.55 4.55 1.44 0.00 0.96 0.44 0.44 -0.70 1.15 -0.32 -0.13 0.00 0.26 -0.58 -0.39 0.51 0.00 0.83 -0.01 -0.05 2.20 0.64 0.00 -0.01 -0.10 0.00 -0.70 0.00 3.49 3.49 -0.31 0.00 -2.56 -1.23 -0.83 1.74 -0.42 -0.35 1.36 0.00 0.54 2.24 0.38 0.32 0.00 -0.98 -0.84 1.99 1.16 1.45 0.00 1.65 -0.65 0.00 1.18 0.00 4.55 4.55 3.32 0.00 1.76 2.69 2.62 -1.00 2.98 0.36 0.29 0.00 -0.22 -0.91 -0.93 1.69 0.00 0 .48 0.47 -1.55 2.69 1.39 0.00 0.54 -2.57 0.00 -0.35 0.00 4.55 4.55 2.09 0.00 -2.78 4.65 6.06 -4.35 3.67 1.29 -1.59 0.00 4.02 -2.46 -0.75 2.97 0.00 1.87 3.18 1.45 2.15 1.80 0.00 -0.70 -5.12 0.00 -4.17 0.00 4.55 4.55 1.16 0.00 0.53 0.23 0.23 -0.12 0.96 0.90 4.01 0.00 0.54 2.53 2.04 0.05 0.00 1.13 0.19 -0.10 -0.16 2.71 0.00 5.58 -3.99 0.00 -0.72 0.00 4.55 4.55 3.66 0.00 1.79 3.71 3.18 -3.66 8.67 -0.41 -1.92 0.00 -0.21 -3.31 -2.18 2.83 0.00 2.25 1.31 -1.17 5.03 2.47 0.00 0.75 -5.01 0.00 -3.54 0.00 4.55 4.55 4.50 0.00 0.40 3.83 3.40 -4.36 7.52 -0.15 -1.59 0.00 0.27 -2.44 -1.29 2.59 0.00 2.36 3.12 -1.05 2.98 2.86 0.00 0.88 -6.11 0.00 -3.89 0.00 4.55 4.55 0.96 0.00 -1.81 4.77 4.96 -2.52 1.47 4.99 -0.03 0.00 0.98 -0.76 -0.97 2.73 0.00 1.00 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-1.43 0.00 -0.86 0.00 0.92 0.92 Simple frequency matrix The columns represent amino acid counts for the amino acid residues from A to Z. The rows represent the alignment positions from 1->n. The file is a "Simple" frequency matrix of "Length" 20 amino acids. The maximum score this matrix can give is 496. The "Threshold" value is an instruction to the profit application to only report matches above the given score. Gribskov profile The columns represent the amino acids from A to Z, the rows denote the alignment position from 1 to n. The last column is the indel penalty. The "Name" is the name used by prophet to refer to the profile, the "Matrix" is the name of the scoring matrix used (containing residue substitution values). "Length" is the length of the alignment. "Max_score" is the maximum score this profile can produce. The threshold is an instruction to prophet to only report hits equal to or above the given value. The gap opening and extension values are used by prophet in the dynamic alignment (Smith Waterman equivalent). Data files The two profile methods require a residue substitution scoring matrix. The Gribskov marices use the data file 'Epprofile' by default. This is derived from a PAM250 scoring matrix. The Henikoff matrices use the data file 'EBLOSUM62' by default. 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 Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other target sequence to the group of aligned probe sequences can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. References 1. Gribskov M, McLachlan AD, Eisenberg D. Proc Natl Acad Sci U S A. 1987 Jul; 84(13): 4355-8. 2. Henikoff S, Henikoff JG. J Mol Biol. 1994 Nov 4; 243(4): 574-8. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description profit Scan one or more sequences with a simple frequency matrix prophet Scan one or more sequences with a Gribskov or Henikoff profile Author(s) Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History 1999 - Written Alan Bleasby. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None