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prophecy |
The profile matrix file can then be used by profit or prophet.
% prophecy Creates matrices/profiles from multiple alignments Input sequence set: ../../data/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 Creates matrices/profiles from multiple alignments Input sequence set: ../../data/globins.msf Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: g Enter a name for the profile [mymatrix]: globins Scoring matrix [Epprofile]: Gap opening penalty [3.0]: Gap extension penalty [0.3]: Output file [globins.prophecy]: |
Go to the output files for this example
Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqset Sequence set USA -type menu Select type -name string Enter a name for the profile * -threshold integer Enter threshold reporting percentage * -datafile matrixf Scoring matrix * -open float Gap opening penalty * -extension float Gap extension penalty [-outfile] outfile Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer First base used -send1 integer Last base used, def=seq length -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 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 set USA | Readable set of sequences | Required | ||||||
-type | Select type |
|
F | ||||||
-name | Enter a name for the profile | Any string is accepted | mymatrix | ||||||
-threshold | Enter threshold reporting percentage | Integer from 1 to 100 | 75 | ||||||
-datafile | Scoring matrix | Comparison matrix file in EMBOSS data path | 'Epprofile' for Gribskov type, or EBLOSUM62 | ||||||
-open | Gap opening penalty | Any numeric value | 3.0 | ||||||
-extension | Gap extension penalty | Any numeric value | 0.3 | ||||||
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.prophecy | ||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
(none) |
!!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: 0.14 Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.15 Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.15 Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.19 Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 0.23 Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.21 Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.10 // 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~~~ |
# 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 PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDASHGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASLDKALAGVANVLAHKYHDAAYQG 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 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 1 0 0 0 2 0 1 0 0 0 0 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# 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 645.45 Threshold 75 Gap_open 3.00 Gap_extend 0.30 Consensus PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG 0.15 0.00 0.03 0.03 0.03 -0.18 0.09 0.06 -0.06 0.00 0.03 -0.09 -0.06 0.00 0.00 0.45 0.09 0.09 0.12 0.09 0.00 0.03 -0.24 0.00 -0.24 0.00 0.87 0.87 0.00 0.00 0.06 -0.06 -0.06 0.18 -0.09 -0.09 0.45 0.00 -0.06 0.24 0.18 -0.09 0.00 -0.06 -0.09 -0.09 -0.03 0.06 0.00 0.33 -0.15 0.00 0.03 0.00 0.87 0.87 0.06 0.00 0.06 -0.06 -0.06 0.06 0.06 -0.09 0.33 0.00 -0.06 0.24 0.18 -0.09 0.00 0.03 -0.06 -0.09 -0.03 0.06 0.00 0.45 -0.24 0.00 -0.03 0.00 0.87 0.87 0.09 0.00 -0.15 0.45 0.30 -0.30 0.18 0.12 -0.06 0.00 0.09 -0.15 -0.12 0.18 0.00 0.03 0.18 0.00 0.06 0.06 0.00 -0.06 -0.33 0.00 -0.15 0.00 0.87 0.87 0.12 0.00 0.06 0.06 0.06 -0.09 0.12 -0.03 0.06 0.00 0.06 -0.03 0.00 0.06 0.00 0.09 -0.03 -0.03 0.09 0.45 0.00 0.06 -0.18 0.00 -0.09 0.00 0.87 0.87 0.18 0.00 0.06 0.18 0.15 -0.18 0.45 -0.06 -0.09 0.00 -0.03 -0.15 -0.09 0.12 0.00 0.09 0.06 -0.09 0.18 0.12 0.00 0.06 -0.30 0.00 -0.18 0.00 0.87 0.87 0.12 0.00 0.18 0.06 0.06 -0.09 0.18 -0.06 -0.03 0.00 0.06 -0.12 -0.09 0.09 0.00 0.12 -0.03 0.03 0.45 0.09 0.00 -0.03 0.09 0.00 -0.12 0.00 0.87 0.87 0.13 0.00 0.13 -0.13 -0.13 0.13 0.13 -0.19 0.69 0.00 -0.13 0.50 0.38 -0.19 0.00 0.06 -0.13 -0.19 -0.06 0.13 0.00 0.94 -0.50 0.00 -0.06 0.00 0.87 0.87 0.59 0.00 -0.06 -0.07 -0.02 0.24 0.31 -0.25 0.68 0.00 -0.20 0.72 0.60 -0.14 0.00 0.14 -0.03 -0.39 0.03 0.23 0.00 0.97 -0.55 0.00 -0.12 0.00 0.87 0.87 0.52 0.00 0.12 0.35 0.35 -0.54 0.38 0.41 -0.22 0.00 0.20 -0.30 -0.22 0.31 0.00 0.76 0.53 0.27 0.61 0.20 0.00 -0.08 -0.38 0.00 -0.48 0.00 0.87 0.87 0.01 0.00 -0.88 -0.10 0.24 0.83 -0.26 -0.04 0.62 0.00 -0.16 1.19 0.96 -0.18 0.00 -0.22 0.11 -0.34 -0.28 -0.02 0.00 0.62 0.07 0.00 0.09 0.00 0.87 0.87 0.54 0.00 0.44 0.37 0.34 -0.45 0.94 -0.20 -0.08 0.00 0.14 -0.40 -0.25 0.35 0.00 0.41 -0.02 -0.08 1.07 0.80 0.00 0.08 -0.38 0.00 -0.51 0.00 0.87 0.87 0.82 0.00 -0.13 0.71 0.92 -0.68 0.80 0.16 -0.20 0.00 0.14 -0.34 -0.20 0.38 0.00 0.56 0.45 -0.09 0.42 0.36 0.00 0.03 -1.13 0.00 -0.61 0.00 0.87 0.87 0.37 0.00 -0.47 0.17 0.38 -0.05 0.14 0.07 -0.26 0.00 0.19 -0.05 -0.22 0.21 0.00 -0.01 0.13 0.35 0.52 0.05 0.00 -0.30 -0.16 0.00 0.01 0.00 0.87 0.87 0.41 0.00 -0.61 0.90 1.26 -0.71 0.55 0.42 0.25 0.00 0.31 0.13 0.15 0.40 0.00 0.26 1.04 0.04 0.05 0.19 0.00 0.49 -1.41 0.00 -0.69 0.00 4.55 4.55 0.13 0.00 -1.04 -0.15 0.01 0.48 -0.39 -0.11 0.51 0.00 0.83 0.99 1.12 -0.01 0.00 -0.10 0.23 0.20 -0.13 0.12 0.00 0.54 0.36 0.00 -0.23 0.00 4.55 4.55 1.00 0.00 0.64 0.24 0.24 -0.41 0.81 -0.30 0.35 0.00 0.13 -0.08 -0.01 0.24 0.00 0.58 -0.09 -0.17 1.23 0.86 0.00 0.56 -0.52 0.00 -0.50 0.00 4.55 4.55 1.09 0.00 -0.33 0.08 0.18 -0.09 0.21 -0.09 0.27 0.00 0.33 0.48 0.58 0.07 0.00 0.55 0.27 -0.09 0.23 0.35 0.00 0.48 -0.45 0.00 -0.42 0.00 4.55 4.55 0.81 0.00 0.28 0.11 0.11 0.02 0.25 0.19 0.96 0.00 -0.14 0.57 0.42 0.00 0.00 0.30 0.09 -0.24 0.04 0.33 0.00 1.16 -1.02 0.00 -0.07 0.00 4.55 4.55 0.18 0.00 -0.48 0.64 0.44 -0.46 0.23 0.20 0.36 0.00 0.51 0.16 0.35 0.23 0.00 0.18 0.36 0.36 0.10 0.44 0.00 0.49 -0.41 0.00 -0.54 0.00 4.55 4.55 0.54 0.00 -0.30 -0.00 -0.00 -0.24 0.14 -0.11 -0.31 0.00 0.85 -0.20 -0.13 0.31 0.00 0.17 0.07 0.74 1.03 0.20 0.00 -0.32 0.34 0.00 -0.23 0.00 4.55 4.55 1.15 0.00 0.04 0.11 0.19 -0.01 0.45 -0.22 0.41 0.00 0.00 0.45 0.45 0.10 0.00 0.39 0.02 -0.39 0.45 0.98 0.00 0.54 -0.54 0.00 -0.27 0.00 4.55 4.55 -0.59 0.00 -1.37 -0.55 -0.60 0.59 -0.70 0.19 -0.64 0.00 0.77 0.14 -0.34 0.60 0.00 -0.65 -0.10 1.43 0.47 -0.35 0.00 -0.90 1.17 0.00 0.70 0.00 4.55 4.55 0.84 0.00 0.10 0.51 0.46 -0.41 0.84 -0.17 0.76 0.00 -0.08 0.37 0.31 0.10 0.00 0.33 0.15 -0.39 0.23 0.43 0.00 1.25 -1.48 0.00 -0.47 0.00 4.55 4.55 0.29 0.00 -0.79 0.77 1.01 -1.00 0.24 0.34 -0.33 0.00 1.52 -0.50 0.03 0.60 0.00 0.59 0.73 0.81 0.39 0.36 0.00 -0.24 -0.67 0.00 -1.02 0.00 4.55 4.55 1.29 0.00 0.37 -0.04 0.02 -0.05 0.55 -0.31 0.87 0.00 -0.23 0.66 0.50 -0.12 0.00 0.39 -0.09 -0.53 0.21 0.43 0.00 1.26 -1.05 0.00 -0.13 0.00 4.55 4.55 0.85 0.00 0.11 0.82 0.60 -0.46 0.53 0.45 -0.20 0.00 0.14 -0.35 -0.33 1.10 0.00 0.04 0.34 -0.27 0.31 0.28 0.00 -0.17 -0.59 0.00 0.08 0.00 4.55 4.55 0.33 0.00 0.22 0.10 0.10 -0.16 0.27 -0.07 -0.03 0.00 0.06 -0.13 -0.09 0.12 0.00 0.19 -0.00 -0.01 0.51 0.15 0.00 -0.00 -0.02 0.00 -0.16 0.00 3.49 3.49 -0.07 0.00 -0.59 -0.28 -0.19 0.40 -0.10 -0.08 0.31 0.00 0.12 0.51 0.09 0.08 0.00 -0.22 -0.19 0.46 0.27 0.34 0.00 0.38 -0.15 0.00 0.27 0.00 4.55 4.55 0.76 0.00 0.40 0.62 0.60 -0.23 0.69 0.08 0.07 0.00 -0.05 -0.21 -0.21 0.39 0.00 0.11 0.11 -0.36 0.62 0.32 0.00 0.13 -0.59 0.00 -0.08 0.00 4.55 4.55 0.48 0.00 -0.64 1.07 1.40 -1.00 0.84 0.30 -0.37 0.00 0.92 -0.57 -0.17 0.68 0.00 0.43 0.73 0.33 0.49 0.41 0.00 -0.16 -1.18 0.00 -0.96 0.00 4.55 4.55 0.27 0.00 0.12 0.05 0.05 -0.03 0.22 0.21 0.92 0.00 0.13 0.58 0.47 0.01 0.00 0.26 0.04 -0.02 -0.04 0.63 0.00 1.28 -0.92 0.00 -0.17 0.00 4.55 4.55 0.84 0.00 0.41 0.85 0.73 -0.84 1.99 -0.09 -0.44 0.00 -0.05 -0.76 -0.50 0.65 0.00 0.52 0.30 -0.27 1.16 0.57 0.00 0.17 -1.15 0.00 -0.81 0.00 4.55 4.55 1.04 0.00 0.09 0.88 0.78 -1.00 1.73 -0.04 -0.37 0.00 0.06 -0.56 -0.30 0.60 0.00 0.54 0.72 -0.24 0.69 0.66 0.00 0.20 -1.41 0.00 -0.90 0.00 4.55 4.55 0.22 0.00 -0.42 1.10 1.14 -0.58 0.34 1.15 -0.01 0.00 0.23 -0.17 -0.22 0.63 0.00 0.23 0.76 0.22 -0.01 0.15 0.00 0.11 -1.12 0.00 -0.21 0.00 4.55 4.55 1.40 0.00 0.14 0.65 0.50 -0.62 0.58 0.00 0.39 0.00 0.14 -0.03 0.11 0.28 0.00 0.46 0.32 -0.15 0.40 0.47 0.00 0.44 -1.03 0.00 -0.47 0.00 4.55 4.55 0.15 0.00 -0.45 -0.28 -0.13 0.99 0.18 -0.35 0.98 0.00 -0.42 1.28 1.00 -0.26 0.00 -0.22 -0.18 -0.60 -0.08 0.14 0.00 1.05 -0.09 0.00 0.15 0.00 4.55 4.55 [Part of this file has been deleted for brevity] 0.16 0.00 -0.11 0.88 0.64 -0.34 0.31 0.88 -0.34 0.00 0.27 -0.44 -0.47 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The Henikoff matrices use the data file 'EBLOSUM62' by default.
Program name | Description |
---|---|
profit | Scan a sequence or database with a matrix or profile |
prophet | Gapped alignment for profiles |