I know you can use Ctrl F to do it, but is there a way to find all those location and once?

I have a similar, though expanded question. I would like to search a sequence with a large number (>300) of short sequences in one go and, ideally, have the hits mapped onto the sequence as an annotation.

Just a update, I still could not find the function within Geneious, hope they can add that on later because it is a very simple and useful thing to have.
Since I can not wait for them to develop the next version or a plug in, I just wrote a small program in Perl and does the job. I will make it available for download later, if any of you are interest in it.

Hi,
You are right, this is a very simple and useful plugin. I have put forward the request to the development team. Though I don't think it will be out before Geneious 3.0.

If you or somebody you know has knowledge in Java you could develop this plugin for Geneious yourself using the public API.

I agree that this would be useful. Our group is searching for an easy-to-use platform to screen for short repeats. I think we'd purchase the 'pro' version if this was added to the next release.

The demand for a feature like this is become increasingly apparent. Due to popular demand we will most likely add this to version 3.0 in a couple of months time.

Our plan is to have the "sequence search" feature annotate all matches in the sequence. Is this the preferred behaviour?

One thing I noticed is that the searches are very strict, i.e. they only look for 100% matches based on the text.

Several implementations in competing software perform searches which allow one to use ambiguity symbols (N, R, Y, S, etc) for nucleotides which allows for more 'fuzzy' matching. Coming from a BioPerl background I'm not sure how hard that would be to implement here.

We are currently working on the ability to locate arbitrary query strings with ambiguity symbols inside a sequence document.

If instead of locating the exact locations inside a document where an ambiguous query string matches, you wanted to search for documents in your local database that match a given ambiguous query string, this would be harder to do because we maintain a search index. However, you can do a blast-like fuzzy search for documents in your local database that contain a sequence similar to your search string. To do this, click "Search" in the toolbar and then select the "Nucleotide Similarity Search" from the drop down list.

In Geneious 3.5, a public beta of which will be released very soon, you will be able to search for subsequences including ambiguities (i.e. a motif search) in both nucleotide and amino acid sequences through the normal find dialog (Ctrl+F).

Hi Guys

I think that with the growing importance and functionality of the find tool it needs to go on a tool bar somewhere.

Revel