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COMPLEX

NAME

complex − Find the linguistic complexity in nucleotide sequences

SYNOPSIS

complex −sequence seqall −lwin integer −step integer −jmin integer −jmax integer −omnia toggle −sim integer −freq boolean −print boolean −outfile outfile −ujtablefile outfile −outseq seqoutall

complex −help

DESCRIPTION

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

OPTIONS

Input section
−sequence
seqall

−lwin integer

Default value: 100

−step integer

Displacement of the window over the sequence Default value: 5

−jmin integer

Default value: 4

−jmax integer

Default value: 6

Advanced section
−omnia
toggle

Calculate over a set of sequences Default value: N

−sim integer

Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases

−freq boolean

Execute the simulation of a sequence based on the base frequency of the original sequence Default value: N

Output section
−print
boolean

Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences Default value: N

−outfile outfile

−ujtablefile outfile

Default value: complex.ujtable

−outseq seqoutall

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).

SEE ALSO

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

AUTHOR

Debian−Med Packaging Team <debian−med−packaging@lists.alioth.debian.org>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

Copyright © 2007 Debian-Med Packaging Team

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.

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