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 "Create new - group" is a quick way to highlight and group residues matching - the specified search pattern throughout the alignment.
-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 at least the specified number of the preceding element. | -
| {min,max} | -Matches if the preceding element matches between min and max - number of times. | -
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 | +