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Search several features at once (Read 6142 times)

Mar 7^th, 2011 at 7:35pm

Agu Offline
Junior Member
(Argentinian)

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Posts: 63

UGENE is capable of searching for a pattern in several sequences with "Search pattern" or "Smith-watherman" algorithm both in Workflow and query designer. Nevertheless, is not possible to search for several features at once.This could be done just being able to select instead of the pattern, a multiple fasta file with the patterns to be looked for. Then they could be annotated using the "fasta name" of each pattern.
This could be useful for annotating several sequences at once with a set of features. Also, it could serve to search and annotate several primers in one sequence. This way you could have a fasta file with 500 primers, and search and annotate all of them at once. I don't know of any program capable of doing that, although it might be useful for a lot of people.

Thanks

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Reply #1 - Mar 9^th, 2011 at 1:41pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Thanks for suggestion, we will put this feature on our TODO list.

Hope it will be available in 1.9.2 already (to be released in the end of March)

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Reply #2 - Jun 23^rd, 2011 at 12:10pm

cusont Offline
YaBB Newbies

Posts: 1

I can search on a specific site. This feature is aviable in advanced search (or I can use "site" command). The problem is that I can search only one site at one moment.
Is there a search engine which allows searching on several sites?

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Reply #3 - Jun 24^th, 2011 at 9:52pm

Agu Offline
Junior Member
(Argentinian)

Gender:
Posts: 63

Yes, you can search one or several features in one or several sequences at the same time. In version 1.9.3 there is a bug and you can't include ambiguous bases, but hopefully it will be fixed soon.

To do that, you need to use the workflow designer.
For example, let's say that you want to search 10 features in 20 different genbank sequences. You will need to have all the 10 features in one file in fasta format:
>feature1
ACCTCTCTCT
>feature2
TGTTGTGT
...

Go to tools/Workflow designer...

Drag and drop the elements that you need from the panel on the left. In this case is very simple, so you only need an element to read the sequence, another to perform the search (Smith-Waterman) and a third one to write the output. Then connect the elements (Read-search-output) and complete the different options for each element (location of files, names to annotate the features, etc.). If you have several sequences, reply no when asked if you want different iterations (that's useful when you want to search different patterns for different sequences, here you will search the same patterns on every sequence). The most important here is that in the Smith-Waterman element, you have to put in "pattern(s)" the path to the file with all the things you want to search in fasta format.

Let me know if it worked or if you need more help.

wd.png (47 KB | )

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