Find
The Find function can also be invoked by pressing Ctrl +
Shift + F (
+ Shift + F on Mac).
The Find function can be used for searching the sequence. Clicking the find button will search for the first occurrence of the search term. Clicking the find button again will find the next occurrence and so on. If the search string is found, the corresponding part of the sequence will be selected.
- Search term. Enter the text to search for. The search function does not discriminate between lower and upper case characters.
- Sequence search. Search the nucleotides or amino acids. For amino acids, the single letter abbreviations should be used
for searching. The sequence search also has a set of advanced search
parameters:
- Include negative strand. This will search on the negative strand as well.
- Treat ambiguous characters as wildcards in search term. If you search for e.g. ATN, you will find both ATG and ATC. If you wish to find literally exact matches for ATN (i.e. only find ATN - not ATG), this option should not be selected.
- Treat ambiguous characters as wildcards in sequence. If you search for e.g. ATG, you will find both ATG and ATN. If you have large regions of Ns, this option should not be selected.
- Annotation search. Searches the annotations on the sequence. The search is performed both on the labels of the annotations, but also on the text appearing in the tooltip that you see when you keep the mouse cursor fixed. If the search term is found, the part of the sequence corresponding to the matching annotation is selected. Below this option you can choose to search for translations as well. Sequences annotated with coding regions often have the translation specified which can lead to undesired results.
- Position search. Finds a specific position on the sequence. In order to find an interval, e.g. from position 500 to 570, enter "500..570" in the search field. This will make a selection from position 500 to 570 (both included). Notice the two periods (..) between the start an end number (see Regions). If you enter positions including thousands separators like 123,345, the comma will just be ignored and it would be equivalent to entering 123345.
- Include negative strand. When searching the sequence for nucleotides or amino acids, you can search on both strands.
- Name search. Searches for sequence names. This is useful for searching sequence lists, mapping results and BLAST results.