Searching in Alignment
To search for a pattern(s) in an alignment, navigate to the Search in Alignment tab within the Options Panel.
The following parameters are available:
Search Context
This group specifies the search context to be used for searching a pattern. It is possible to search for patterns in sequences or sequence names.
Search Pattern
To search for a pattern(s), input the value you want to search in the text field.
Press the Next button to search in the direction “From left to right, from top to bottom.” Press the Previous button to search in the direction “From right to left, from bottom to top.” If the pattern is found, the result will be focused on and highlighted in the Sequence area. You can continue the search in any direction from this position.
To group results, press the Group button. The results will be selected and grouped at the top after the first click or at the bottom after the second click of the button.
Search Algorithm
This group specifies the algorithm to be used to search for a pattern. The algorithm can be one of the following:
- InsDel — There could be insertions and/or deletions, i.e., a pattern and the searched region can vary in their length. You can specify the percentage of the pattern and a searched region match in the field nearby. Note that this value also depends on the pattern length and is disabled when the pattern hasn’t been specified.
- Substitute — A pattern may contain characters different from the characters in the searched region. When this algorithm has been selected, you can also specify the match percentage, and additionally, it is possible to take into account ambiguous bases.
- Regular Expression — A regular expression may be specified instead of a pattern. For example, the character ‘.’ matches any character, ‘.*’ matches zero or more of any characters. There is also the Limit result length option that specifies the maximum length of a result.
- Exact — Find a place where one or several patterns are found within a larger pattern.
Search In
In this group, you can specify the sequence range where to search for a pattern. You can search in the whole alignment, specify a custom region, or search in the selected region.
Other Settings
This group contains additional common settings:
Remove overlapped results — Annotates only one of the overlapped results.
Limit results number to — Limits the number of the searched results to the specified value.