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Documentation for PeptideCutter Peptide
searches a protein sequence from the SWISS-PROT and/or TrEMBL
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 to provide
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 top of 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,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
All or a group of favourite enzymes
and chemicals can be selected. Most of the cleavage rules for individual
were deduced from specificity data summed up by Keil (1992). Please
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.
2.3. Display of results
Different options for the result display are available:
The first two options imply the creation of a list of all detected cleavages.
- The first list is arranged alphabetically according to enzyme names.
- The second list displays sequentially all cleavage sites in the sequence
and the respective cleaving enzymes from the N- to the C-terminus. In addition
to this, a list of peptides resulting from the digestion is provided,
the respective lengths in amino acids and the molecular weight in Daltons (using average masses and showing peptides in ion mode [M]).
The peptides displayed are calculated in a way of assuming that all chosen
enzymes are present during digestion. If you want to have a list of
peptide resulting from the cleavage of only one enzyme or chemical, please
select only the respective enzyme and deselect the others.
Please be aware of the fact that the present version of the PeptideCutter program does not take into consideration any kind of modification neither of the protein sequence nor of modifications evoked by the cleavage. If you are interested in a more sophisticated analysis of the resulting peptide, we recommend to use the PeptideMass program.
- Finally, there is also the possibility to show all results using a map. The entered protein sequence is marked with a "|" above an amino acid when there is a cleavage site between this amino acid and the neighbouring amino acid in C-terminal direction (i.e. directly on the "right side" of the marked amino acid).
The sequence map is displayed in portions of 10 to 60 amino
acids. It is possible to modify the portion size and thus the map
output according to his needs. Adjusting this size may be especially important
when printing out the map. In addition to this, it is possible to consider
only enzymes for the output that cut the sequence a chosen number of times. When
the results are displayed in form of a map,
one enzyme of choice can be selected by mouseclicking. The sites that are potentially cleaved
by this enzymes are then displayed in a separate window.