I have been using the Unipro Ugene 1.42 for some time and really like the application.  But upon upgrading to 1.5, I am unable to do HMM search using either HMM 2.3 or HMM 3.  Also tried the Congene it can't even display help menu (congene --help.

Hi Weiting Ni,
please tell us the version of UGENE which you use: win, linux, mac and how to reproduce the crash with HMMs.

In case of linux please also specify the installed Qt version.

Thanks for your reply.

I installed Unipro Ugene 1.5 Windows version in both my office and home computers.  Both computers are running Windows XP SP3.  As soon as I start the search, an error widnow pops up, and the application exit when I click the "OK" button.  I also tried the Congene at the command line "congene.exe --help" on my office computer, it produced same error window.

I have removed 1.5 and reverted back to 1.42.

Again, thanks for the very useful program.

Weiting

Hi Weiting, thanks for your report!
We've fixed crash in congene, and also fixed a crash in HMM3 caused by malformed HMM file. This fixes will be available in UGENE 1.5.1 which will be released during this week.

It's still unclear for us how to reproduce the crashes in HMM search you are talking about. Please consider this steps:

1) Before installing UGENE 1.5, completely remove old versions of UGENE. Also, please ensure that you have no UGENE settings file in the following path:
C:\Documents and Settings\%username%\Application Data\Unipro
If UGENE.ini exists here, just remove or rename it.

2) After installing UGENE 1.5 on the clear of old UGENEs system, try to reproduce the crash with HMM search.

3) If the crash still persist, please send us the sequence and the hmm file you are trying to search. Do I understand correctly that you are doing the following:
1) start UGENE
2) open the document (with button open)
3) open any of HMM2 or HMM3 search dialogs
4) specify the HMM file
5) press the 'search' button
?

I have removed all the unipro related entries in regedit as well as the folder you mentioned after uninstalled the software.  Re-installed unipro 1.5.  The HMM 3 search is not working.  Attached is the debug message.

Weiting

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As I mentioned above, HMM3 crashes if started with bad HMM file. It looks like HMM3 currently doesn't support HMMs built with HMMER2 (or our HMM2 tool, which are almost the same).

So, I suggest you to try to launch HMM3 with HMM profiles built with HMM3. If UGENE crashes with such models please send us them so we can reproduce the crash.

Again, thanks for reports!

Thanks for the quick reply.  I was able to build a HMM3 model.  However search against the model did not produce any result (no file created).  The search went very fast (couple second even with a large sequence file)

Well, I think that such result is a consequence of differencies between HMMER2 and HMMER3.

I suggest you to look at this post at Eddy's blog: http://selab.janelia.org/people/eddys/blog/?p=117
and to consult with HMMER3 user guide: ftp://selab.janelia.org/pub/software/hmmer3/Userguide.pdf

Userguide can give you some clues about configuring hmmbuild and hmmsearch from HMM3. Also, we can almost gurantee that our HMM3 will produce the same results as the original HMMER3 package since we carefully tested them for compatibility.

Ivan,

Sorry I probably did not make my self clear.  I was able to build HMMER3 model, but failed to produce result when searching sequences against the model using HMMER search. I used default parameters for building the model and searching.

The result was displayed in the object panel but it contain no data in the sequence panel.

Thanks for all your help

Weiting

Well, if I understand you correctly, it is the normal UGENE behaviour - it just means that no results were found (sequence contains no hmmer signals of a given model). You can check task report to see the actual number of results.

So, if you have results found by HMMER2 and no results by HMMER3 with models built from one MSA it is the difference between HMMERs.

Take a look at the attached screenshot.

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