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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: 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]:
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 [-outf] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||||
---|---|---|---|---|---|---|---|---|---|
[-sequence] (Parameter 1) |
Sequence set USA | Readable 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 | ||||||
[-outf] (Parameter 2) |
Output file name | Output file | <sequence>.prophecy | ||||||
Optional qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced qualifiers | Allowed values | Default | |||||||
(none) |
The one used in the example is:
!!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~~~
The one produced by the above example is:
# 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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Program name | Description |
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profit | Scan a sequence or database with a matrix or profile |
prophet | Gapped alignment for profiles |