SYNOPSIS

pepdigest -seqall seqall -mwdata datafile -menu list -mono boolean -unfavoured boolean -ragging boolean -termini list -overlap boolean -allpartials boolean -outfile report

pepdigest -help

DESCRIPTION

pepdigest

OPTIONS

Input section

-seqall seqall

-mwdata datafile

Molecular weight data for amino acids Default value: Emolwt.dat

Required section

-menu list

Default value: 1

-mono boolean

Default value: N

Advanced section

-unfavoured boolean

Trypsin will not normally cut after 'KR' if they are followed by any of 'KRIFLP'. Lys-C will not normally cut after 'K' if it is followed by 'P'. Arg-C will not normally cut after 'R' if it is followed by 'P'. V8-bicarb will not normally cut after 'E' if it is followed by any of 'KREP'. V8-phosph will not normally cut after 'DE' if they are followed by 'P'. Chymotrypsin will not normally cut after 'FYWLM' if they are followed by 'P'. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones.

-ragging boolean

Allows semi-specific and non-specific digestion. This option is particularly useful for generating lists of peptide sequences for protein identification using mass-spectrometry.

-termini list

Default value: 1

Output section

-overlap boolean

Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it.

-allpartials boolean

As for overlap but fragments containing more than one potential cut site are included.

-outfile report

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.