digest

digest

digest finds the positions where a specified proteolytic enzyme or reagent might cut a peptide sequence.

Here is a sample session with digest:

% digest Input sequence: sw:opsd_human Enzymes and Reagents          1 : Trypsin          2 : Lys-C          3 : Arg-C          4 : Asp-N          5 : V8-bicarb          6 : V8-phosph          7 : Chymotrypsin          8 : CNBr Select number [1]: Output file [opsd_human.digest]:

Mandatory qualifiers:

[-sequencea] (sequence)

Sequence USA.

-menu (menu)

Select number.

[-outfile] (report)

Output report filename.

Advanced qualifiers:

-unfavoured (boolean)

Trypsin will not normally cut after a K if it is followed by another K or a P. Specifying this shows those cuts as well as the favoured ones.

-aadata (string)

Molecular weight data for amino acids.

-overlap (boolean)

Used for partial digestion. Shows all cuts from favoured cut sites plus 1-3, 2-4, 3-5, etc. Overlaps are fragments with exactly one potential cut site within them (e.g., 2-5 is invalid).

-allpartials (boolean)

Similar to overlap, but fragments containing more than one potential cut site are included.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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