Pattern Search
You can search for Patterns of Amino Acids in the protein translation by selecting 'Pattern Search' from the 'Protein' pull down menu. Existing patterns can be selected from the list or
new patterns added by pressing the 'Add Pattern' button. After pressing the 'Search' button a list of hits, if any, for the selected pattern is displayed. Press the 'Location' button to reveal
the location of a selected hit in the protein sequence or 'Add Match to Annotation Box' to enter the hit in the 'Annotation Box'.
Pattern Syntax;
Amino acids are enclosed within square brackets []
The pattern [P][ST] would therefore search for a P followed by either an S or a T
The character ^ is used to exclude Amino Acids
The Pattern [^DE][P][ST] would therefore search for a P followed by either an S or a T as long as the P was not proceeded by a D or an E.
The character * is used as a wildcard to represent any amino acid
The Pattern [P][*][P] would therefore search for a Proline followed by any other amino acid followed by another Proline
A character definition such as [ST] followed by {} is used to define repetition where
{x} is exactly x times
{x,} is at least x times and
{x,y} is at least x but not more than y times
The Pattern [KR]{4,} would find occurrences of 4 or more adjacent Ks or Rs (eg KRKR, RRKKR, but not KRK)
The Pattern [DE][ST][*]{4,7}[W] would find a D or E followed by an S or T as long as a W was within 4-7 amino acids of the S or T