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prophecy |
Please help by correcting and extending the Wiki pages.
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.
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.
% 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]:
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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]:
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Go to the output files for this example
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
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| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-sequence] (Parameter 1) |
seqset | (Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||
| -type | list | Select type |
|
F | ||||||
| -datafile | matrixf | Scoring matrix | Comparison matrix file in EMBOSS data path | 'Epprofile' for Gribskov type, or EBLOSUM62 | ||||||
| -name | string | Enter a name for the profile | Any string | mymatrix | ||||||
| -threshold | integer | Enter threshold reporting percentage | Integer from 1 to 100 | 75 | ||||||
| -open | float | Gap opening penalty | Any numeric value | 3.0 | ||||||
| -extension | float | Gap extension penalty | Any numeric value | 0.3 | ||||||
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.prophecy | ||||||
| Additional (Optional) qualifiers | ||||||||||
| (none) | ||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||
| (none) | ||||||||||
| Associated qualifiers | ||||||||||
| "-sequence" associated seqset qualifiers | ||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||
| -sid1 -sid_sequence |
string | Entryname | Any string | |||||||
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||
| -fformat1 -fformat_sequence |
string | Features format | Any string | |||||||
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||
| "-outfile" associated outfile qualifiers | ||||||||||
| -odirectory2 -odirectory_outfile |
string | Output directory | Any string | |||||||
| General qualifiers | ||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||
!!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~~~
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# 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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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 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 1 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 939.76 Threshold 75 Gap_open 3.00 Gap_extend 0.30 Consensus PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG 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 1.13 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 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0.00 0.74 0.41 -0.61 1.10 0.82 0.00 0.41 -1.92 0.00 -1.04 0.00 0.92 0.92 -0.43 0.00 1.43 -0.71 -0.71 1.86 -0.86 0.43 0.14 0.00 -0.86 0.43 -0.14 -0.14 0.00 -1.14 -0.86 -0.86 -0.57 -0.43 0.00 -0.14 1.57 0.00 2.14 0.00 0.92 0.92 0.29 0.00 -0.86 0.86 0.86 -1.14 0.29 0.86 -0.43 0.00 0.57 -0.14 0.00 0.57 0.00 0.43 2.14 0.57 -0.14 -0.14 0.00 -0.29 -0.71 0.00 -0.86 0.00 0.92 0.92 0.86 0.00 0.29 0.86 0.71 -0.86 2.14 -0.29 -0.43 0.00 -0.14 -0.71 -0.43 0.57 0.00 0.43 0.29 -0.43 0.86 0.57 0.00 0.29 -1.43 0.00 -0.86 0.00 0.92 0.92 |
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.
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).
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:
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.
| 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 |
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