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cleave

PURPOSE ^

% Cleave a peptide @var{sequence} using the @var{pattern} at the

SYNOPSIS ^

function [fragments, s, lengths] = cleave (seq, pattern, pos, varargin)

DESCRIPTION ^

% -*- texinfo -*-
% @deftypefn {Function File} {@var{fragments} =} cleave (@var{sequence}, @var{pattern}, @var{position})
% @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}] =} cleave (@dots{})
% @deftypefnx {Function File} {[@var{fragments}, @var{cuttingsites}, @var{lengths}] =} cleave (@dots{})
% @deftypefnx {Function File} {[@dots{}] =} cleave (@dots{}, 'PartialDigest', @var{prob})
% Cleave a peptide @var{sequence} using the @var{pattern} at the
% @var{position} relative to the pattern.  The @var{sequence} is a
% sequence of amino acids; the @var{pattern} is a regular expression to
% find the location of the cleavage; and the @var{position} is the
% position relative to that regular expression (0 is immediately to the
% left of the first character, 1 is immediately to the right of the
% first character, @dots{}).
%
% Example regular expressions for some commone proteases are given
% below.
%
% @multitable @columnfractions .5 .3 .2
% @item Protease @tab Peptide Pattern @tab Position
% @item Trypsin @tab [KR](?~P) @tab 1
% @item Chymotrypsin @tab [WYF](?~P) @tab 1
% @item Glutamine C @tab [ED](?~P)  @tab 1
% @item Lysine C @tab [K](?~P)  @tab 1
% @item Aspartic acid N @tab D @tab 1
% @end multitable
%
% @seealso{rebasecuts, restrict, seqshowwords, regexp}
% @end deftypefn

CROSS-REFERENCE INFORMATION ^

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