prophecy (1e)

Create frequency matrix or profile from a multiple alignment

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  4. prophecy: Create frequency matrix or profile from a multiple alignment

SYNOPSIS

prophecy -sequence seqset -type list -datafile matrixf -name string -threshold integer -open float -extension float -outfile outfile prophecy -help

DESCRIPTION

prophecy is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s).

OPTIONS

Input section

-sequence seqset

-type list

Default value: F

-datafile matrixf

Default value: @($(type) = G: Epprofile H: EBLOSUM62 F: EBLOSUM62)

Required section

-name string

Default value: mymatrix

Profile type specific options

-threshold integer

Default value: 75

Gap options

-open float

Default value: 3.0

-extension float

Default value: 0.3

Output section

-outfile outfile

BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

RELATED TO prophecy…

prophecy is fully documented via the tfm(1) system.

AUTHOR

Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.