In the STALKER window, you can type in a peptide sequence and then search for identical or homologous sequences in proteins
contained within a defined dataset, or against the entire UNIPROT.
You can now use wildcard residues, by indluding "*" if you want to search for a fuzzy motif. This could be N*T or N*S if you wish to look for
potential N-glycosylation sites in a proteome.
RIGHT-CLICK on any protein to set it as a reference protein.
RIGHT-CLICK and select "calculate identity distance" to calculate the Needleman-Wunsch distance between the reference protein and all
other proteins listed. (Note that this value highlights the homology between the proteins and not between the target peptide sequence. The
latter is in the "Identity distance" column.)
Notice in the below figure, that the N-W distance is 0 for dynein, the selected reference protein.
Another way to activate the STALKER feature is to RIGHT-CLICK on an identified peptide in one of the result windows following a
standard search. From the drop-down menu you can then choose to find homologues to this peptide either across UNIPROT or the
currently defined search space.
In the example below, we have recognised calreticulin from a human sample. We have selected the high-scoring peptide
FYALSASFEPFSNK from the result-list and RIGHT-CLICKED on it to forward the sequence to STALKER. From the low N-W
distances we observe that calreticulin is well conserved across the listed proteins.