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TSTanabe / HMSS2

HMSS2
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Patterns file HMSS2 #3

Closed ckeuschn closed 5 months ago

ckeuschn commented 5 months ago

Hi, I just started to explore this great tool, thanks a lot! Does the pattern file for the new version of the software also include the organosulfur pathways? And is there an option to output all proteins or keywords in the database or does one have to define it by hand with for example the -dfk option? Thanks a lot Christoph

TSTanabe commented 5 months ago

Dear Christoph,

currently you can only View and modify the Patterns File via an Editor. You can find IT in the src folder of HMSS2 and add the Patterns you require. I dont know why I did not think of adding an option to print the patterns earlier. Will be included in the next Update. I am currently also working on the implementation of a method to automatically detect gene clustern from the hmmsearch results. Let me know If I can help

Best

Sebastian

ckeuschn @.***> schrieb am Mo., 3. Juni 2024, 17:03:

Hi, I just started to explore this great tool, thanks a lot! Does the pattern file for the new version of the software also include the organosulfur pathways? And is there an option to output all proteins or keywords in the database or does one have to define it by hand with for example the -dfk option? Thanks a lot Christoph

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ckeuschn commented 5 months ago

Hi Sebastian,

thanks for your answer, I will modify the patterns file accordingly. I think it is great that one can use the created database to generate all kinds of output. For some users a general "all_hmms_vs_all_genomes" matrix output could be interesting to get an overview when you start out on a dataset. Great that you keep on working and improving that, definitely will use it :)

Christoph