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EMBOSS: prophecy |
% prophecy
Mandatory qualifiers (* if not always prompted): [-sequence] seqset Sequence set USA -type list 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) |
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 integer value | 3.0 | ||||||
-extension | Gap extension penalty | Any integer 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) |
Program name | Description |
---|---|
cons | Creates a consensus from multiple alignments |
profit | Scan a sequence or database with a matrix or profile |
prophet | Gapped alignment for profiles |