Search
-The search box can be displayed by pressing the keys Control and F or selecting - "Search"
-Note: -Using the "Create new group" is a quick way to group and highlight - residues with the specified search pattern throughout the alignment.
-The search allows regular expression matching.
--
| . | -Any single character. | -
| [] | -Any one of the characters in the brackets | -
| ^ | -The start of a line (column 1). | -
| $ | -The end of a line | -
| * | -Matches zero or more of the preceding characters or expressions. | -
| ? | -Matches zero or one of the preceding characters or expressions. | -
| + | -Matches one or more of the preceding characters or expressions. | -
| {count} | -Matches the specified number of the preceding characters or expressions. - | -
| {min,} | -Matches at least the specified number of the preceding characters or - expressions. | -
| {min,max} | -Matches between min and max of the preceding characters or expressions. | -
Search
+The search box is displayed by pressing Control and F or + selecting "Find..." from the "Search" menu.
+
+"Find next" will find the next occurence of the specified and adjust + the alignment window view to show it, and "Find all" highlights all + matches for a pattern. The "New Feature" is a quick way to highlight + and group residues matching the specified search pattern throughout the alignment. +
Creating Features from Search Results
++ If "New Feature" is selected, the feature can be given a name from + a popup input box. Use the "Feature Settings" under the "View" + menu to change the visibility and colour of the new sequence feature.
+A quick Regular Expression Guide
+A regular expression is not just a simple text query - although it +can be used like one, the query is not parsed literally, but +interpreted like a series of instructions defining the features of the +match. For example, a simple query like "ACDED" would +match all occurences of that string, but "ACD+ED" matches +both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query +"[ILGVMA]{;5,}" would find stretches of small, +hydrophobic amino acids of at least five residues in length. +
+ The table
+below describes some of the regular expression syntax:
| Regular Expression Element | +Effect | +
| . | +Matches any single character | +
| [] | +Matches any one of the characters in the brackets | +
| ^ | +Matches at the start of an ID or sequence | +
| $ | +Matches at the end of an ID or sequence | +
| * | +Matches if the preceding element matches zero or more times | +
| ? | +Matches if the preceding element matched once or not at all | +
| + | +Matches if the preceding element matched at least once | +
| {count} | +Matches if the preceding element matches a specified number of + times + | +
| {min,} | +Matches of the preceding element matched at least the + specified number of times | +
| {min,max} | +Matches if the preceding element matches min or at most max + number of times | +