Hello,

I recently found UGENE looking for alternatives to command prompt-like programs avaliable. So, the first thing is to thank you making avaliable this little gem 

Ok, now the subject. I´m trying to use the hmmer tools to find hmmer signatures in a sequences aa file (fasta) with both, hmmer3 search and phmmer.

The problem(s) I have found is: it load all the sequences (+35000) in the objects tab (upper left window), but only the first 14 in the viewer (upper right window). So, it only perform the search on those, right?
Anyway, I have to add manually any further seq to perform the analysis, which is quite inconvenient. Am I doing it in the right way? Searching hmmer for single seqs works like a charm, but I have no luck with the "batch" searches.
Moreover, if I could finish a search in all the seqs, how to filter them for positive matches?

I also tried the workflow designer. It works for single seq files but return errors for the full sequences file.

So, is there any way(s) to do this kind of batch hmmer search using a long sequence list and how to filter results?

Thank you in advance

Hi,

I attached 3 screenshots: first is the workflow (and errors)  I build using the web documentation about "search sequences with profile hmm"; screenshots 1 and 2 are when I load the fasta file with more than 35000 seq (it only loads 14 in the viewer) and after I added manually one of them (positive) to perform the hmmer search with a pfam profile.
I cannot attach the fasta (very big) and hmmer profile files here but can provide download links if needed.
My question about filtering results is, supposing it can search for the whole list (screenshot1), how to get only the signal-positives? (if possible).

Any advice about how to do correctly the task?

Thank you

Hello,

Thank you very much, your workflow file did the trick. I was misunderstanding how the program works. Also, I need more practice with it.

Thank you for the help and great support!