Find
The Find function can be used for searching the sequence and is invoked by pressing Ctrl + Shift + F (
+ Shift + F on Mac). Initially, specify the 'search term' to be found, select the type of search (see various options in the following) and finally click on the Find button. The first occurrence of the search term will then be highlighted. 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 or number 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. Search 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.
The option "Include translations" means that you can choose to search for translations which are part of an annotation (in some cases, CDS annotations contain the amino acid sequence in a "/translation" field). But it will not dynamically translate nucleotide sequences, nor will it search the translations that can enabled using the "Nucleotide info" side panel.
- Position search. Find 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. 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. Search for sequence names. This is useful for searching sequence lists and mapping results for example.