PeptideCutter

Documentation for PeptideCutter Peptide Characterisation Software:

1. Introduction:

PeptideCutter searches a protein sequence from the SWISS-PROT and/or TrEMBL databases or a user-entered protein sequence for protease cleavage sites. Single proteases and chemicals, a selection or the whole list of proteases and chemicals can be used. Different forms of output of the results are available: Tables of cleavage sites either grouped alphabetically according to enzyme names or sequentially according to the amino acid number. A third option for output is a map of cleavage sites. The sequence and the cleavage sites mapped onto it are grouped in blocks, the size of which can be chosen by the user. This should help the user to find a convenient form of print-out.

2. Using PeptideCutter:

In the program there are a number of fields that must be filled in. In the following, these fields are described, from the topof the form to the bottom.

2.1. Protein Sequence to be Cleaved

In order to provide the program with a sequence the full sequence can be transfered into the first textbox.

Attention: The program accepts the complete input as one single sequence, even if several are entered.
Numbers and space characters are neglected.

If a sequence in FASTA format is entered, the first line is neglected during further steps of the program.

If letters are entered that do not determine an amino acid (B,J,O,U,X or Z) the user will be asked for correction.

The program is case insensitive.

Alternatively, an identifier or an accession number for a protein sequence stocked in the SWISS-Prot or the TrEMBL database can be entered.

Also here, only one sequence can be treated per time

2.2. Enzymes or Reagents to Use for Cleavage

The user has the possibility to select all or a group of favourite enzymes and chemicals. Most of the cleavage rules for individual enzymes were deduced from specificity data summed up by Keil (1992). The user of PeptideCutter should be aware of the fact, that in most cases, the PeptideCutter program makes use of relatively simple rules.
Only in few cases, specificity data allowed the establishment of more sophisticated models, e.g. for trypsin or chymotrypsin. In this case, the cleavage probability of the individual sites is added to the results.