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how to export HMM search result with e-value and score (Read 8447 times)
Aug 11th, 2009 at 4:20am

sp   Offline
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I am using UGENE HMM search function and found it very helpful. But I have problem to export the HMM search results with e-value and score to a text file which I can open with microsoft excel to sort.

Would you please instruct me how to export the HMM search results?

Thanks.
SP.
 
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Reply #1 - Aug 12th, 2009 at 5:06pm

Anton Baskanov   Offline
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Unfortunately there is no way to export annotations as text in current version. This feature will be included in the next release.
 
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Reply #2 - Aug 13th, 2009 at 12:50am

Weiting Ni   Offline
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I have written a simple PHP script to extract the e-value and score to a text file.  Not very pretty (I only spent about an hour to write the script).  The script has three variants, one for uniprot sequences, one for sequences obtained from NCBI and one for my own sequences.

To the software author,  is there a way to skip the sequences without e-values while saving the result?

Thanks.
 
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Reply #3 - Aug 13th, 2009 at 12:45pm

Anton Baskanov   Offline
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No, there is no way to skip the sequences.
 
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Reply #4 - Aug 13th, 2009 at 11:25pm

sp   Offline
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I found out the E-value and score were saved in *.gb file which can be opened by text editor. I wrote a perl script to parse this info out. If this simple feature can be implemented into UGENE, it will be super. Thanks. sp
 
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