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Filter sequences with matching Motif (Read 5028 times)
Sep 27th, 2012 at 12:58am

AK   Offline
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Hello All,

I have a set of protein sequences ~ 600 and I need to filter those with matching motifs (3 nos.). Is there any way I can do this on Ugene.

I am new to ugene and need your help. Thanks

Atul
 
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Reply #1 - Jan 14th, 2013 at 10:30am

Jessie Sun   Offline
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It is really a good idea
 
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Reply #2 - Jan 16th, 2013 at 2:49pm

Yuriy Vaskin   Offline
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Hello!

To do that you need to use Workflow Designer.

I've attached a scheme for that task. I'm going to put it to sample schemes of UGENE so anyone can use it.

Just open the attached scheme and set up the following parameters:

1. In Read Sequence element select the input file(s) - your protein sequences.

2. In Find Substring element set patterns ( semicolon separated list of patterns) - your motifs.

3. In Write Sequence element set the output file.

That scheme reads all your sequences, finds listed pattern in them and mark those sequences that have a motif of interest (number of annotations with name motif_of_interest >=1 ), it passes to the output only the sequences that has a motif.

You may play with the parameters of the elements of the scheme to see what will happen. These chapters of documentation might help: http://ugene.unipro.ru/documentation/wd_manual/index.html
http://ugene.unipro.ru/documentation/wd_manual/workflow_elements/data_flow/marke...
http://ugene.unipro.ru/documentation/wd_manual/workflow_elements/data_flow/marke...
http://ugene.unipro.ru/documentation/wd_manual/workflow_elements/basic_analysis/...
 

motifs.jpg (63 KB | )
motifs.jpg
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