digest

Function

Description

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

This programs allows you to input a protein sequence and to specify one proteolytic agent from a list. It will then output a file containing the positions where the agent cuts, together with the peptides produced.

Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying the qualifier -unfavoured shows those cuts. as well as the favoured ones.

If you wish to emulate a partial digestion, then using the -overlap qualifier will display the results from a digest in which all cut sites are used and in which one site at a time is not cut. Thus the resulting peptide fragments from the cut sites numbered 1, 2, 3, 4 etc. are shown, plus the fragments produced by cutting at the sites 1..3, 2..4, etc.

i.e. fragments containing one potential cut site are also shown.

If you wish to emulate a very partial digestion (!) then using the -allpartials qualifier will do what -overlap did, but also show all possible fragments from using all possible combinations of cut sites. For example, fragments from the cut sites numbered 1, 2, 3, 4, 5 and from the fragments produced by cutting between sites 1..3, 1..4, 1..5, 2..4, 2..5, 3..5, etc.

i.e. fragments containing one or more potential cut site are also shown.

If the boolean -ragging is specified then terminal break-up fragments are also shown; this can be useful for mass spectrometry. Ragging is further controlled by the -termini option which allows you to select removal of residues from the N and/or C termini.

Usage

Command line arguments


Input file format

Any protein sequence.

Output file format

By default digest writes a 'seqtable' report file.

The header information contains the program name, date of run, name of the reagent used to digest the protein and the number of fragments reported. The header will report if complete or partial digestion was chosen.

The rest of the file consists of columns holding the following data:

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

Author(s)

History

Target users

Comments