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Some (several) suggestions (Read 1181 times)
Apr 20th, 2021 at 5:45pm

ANTOINE   Offline
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France

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Posts: 24
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Great update and great improvement of alignment tools!!
I will test all new functions, but the possibility to manage gap during translation of alignment is a great great improvement. (and the update software works perfectly on ubuntu).

I take the opportunity to suggest some (several) improvements , mainly on the interface. Due to qualities and versatility, Ugene is my army-Swiss knife for bioinfo and molecular bio management, and R is now just used for Deseq, proteomic, or metadata.  I have converted several collaborators to Ugene and collect some idea.

My suggestions come from several years of use , mainly on alignments and construction (cloning) PCR,... are totally unaware from surrounding coding difficulties and above all a will to improve this excellent Ugene.

- project view (my main suggestion):

- the main problem is that it's not possible to rearrange the data within project. It seems that data/sequence etc... are by input/creation order.
The possibility to reorder manually or automatically (alphabetical, type) could be a great improvement.

- search in project : the search is only on loaded data, I think that a search on unloaded  should be great.

- Maybe also the possibility to export the project and the sequences in a "package" to send to a collaborator.


-Alignements:

-  for large and long alignment, it could be usefull to have the possibility to put markers on alignment (to identify genomic features as splicing site, exon, RE,...).

- Have a annotation like for single sequence (gb)?

- A possibility to translate with the ambiguous genetic code (IUPAC), I prefer trash bad sequences, but for historical is difficult.

- primer database:

- the database is quickly overflowed and useless because it could be a pain if database contains more than 50 primers which is not a large numbers (I have more than 250 primers in my boxes).  I stop to use  by consequences.

     I have no evident solutions but suggestions:
     
     - database specific to project
     - database with folders
     - additionnal primer info and search interface: target (gene, species), restriction site,...type (sanger, crispR,..))
     



- sequence details view:

     + wrap/unwrap sequence: the possibility to set by default a type (in one line or cut on several line ) should be include in preference because when you work on DNA sequence with 6 tranlated frame it difficult to follow translation (maybe my brain is not designed for sequence on several lines).
This point is critical when you analyse dotplot with two sequences on the screen two follow for example DNA mutation and check if they are sysnonimous or not or affect DNA/RNA parterns.
     
- screens/windows : I have a reasonable sized screen (24 inch 16:9) with a second screen and  I have difficulties see all sequence windows, especially if the main windows is a plasmid, a dotplot ...

suggestions:

     - the possibility to close the annotation view (fully)

     - the possibility to order/move windows like sequence detail.. ,

     is it  not possible to have windows out of main ugene windows? (usefull with with several screen )
     
     
- Force In silico PCR:
It is possible to have degenerate primers for mutagenesis but it is not possible to force PCR  (find product anyway) with primers with devoiding to much to dimers formation, Tm,GC% ..

For example is not possible to simulate direct mutagenesis with two overlapping primes (S /AS). Moreover, often we do not chose the region to amplify/mutate/sequence, and it could be GC deviant for example.


Future?:

- Guide cloning/shRNA: We used synthetic hybrided oligos which not contain restriction site but just cohesive end.
Maybe a tool to design CRispR guide.

- recombinase cloning: it seems that it's a emerging technology,  a tools to design (and to virtual clone) could be usefull

- R/bioconductor interaction (probably not trivial but will place Ugene at the level of G... ) ? : DEseq and proteomic (MS/MS analysis), improvement of data visualization ?


It's not a definitive list  Roll Eyes  , I'm sure that the new features give new ideas. If my suggestion list is too long, I apologize.

Thanks a lot for Ugene!
Antoine
 
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Reply #1 - Apr 26th, 2021 at 9:56am

Dmitrii Sukhomlinov   Offline
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Russia

Gender: male
Posts: 53
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Hello,

Thank you for your  suggestions, we discussed them and decided to implement the following:

- project view (my main suggestion):

- the main problem is that it's not possible to rearrange the data within project. It seems that data/sequence etc... are by input/creation order.
The possibility to reorder manually or automatically (alphabetical, type) could be a great improvement.
---- https://ugene.dev/tracker/browse/UGENE-7202 Object reordering in Project View by drag'n'drop

- search in the project: the search is only on loaded data, I think that a search on unloaded should be great.
---- This feature has no sense since we get rid of the opportunity to unload objects from the project.

- Maybe also the possibility to export the project and the sequences in a "package" to send to a collaborator.
---- https://ugene.dev/tracker/browse/UGENE-7203 - new menu action "Export project with data"


-Alignments:

- for large and long alignment, it could be useful to have the possibility to put markers on alignment (to identify genomic features as splicing site, exon, RE,...).
---- https://ugene.dev/tracker/browse/UGENE-7205 - add 2D markers. This is a large and difficult feature, I don't this that it'll be implemented in the nearest future.

- Have an annotation like for a single sequence (gb)?
---- https://ugene.dev/tracker/browse/UGENE-7204 - add annotations to Alignment Editor. The same.

- A possibility to translate with the ambiguous genetic code (IUPAC), I prefer trash bad sequences, but for historical is difficult.
---- This is not clear to me. Could you, please, describe in more detail this suggestion.

- primer database:

- the database is quickly overflowed and useless because it could be a pain if a database contains more than 50 primers which are not large numbers (I have more than 250 primers in my boxes). I stop to use by consequences.

   I have no evident solutions but suggestions:
   
   - database specific to project
   - database with folders
   - additional primer info and search interface: target (gene, species), restriction site,...type (sanger, crispR,..))
---- https://ugene.dev/tracker/browse/UGENE-7206 - Create the "Choose primer library" setting in the "Primer library" window. We decided to choose the second option from your list? as far as the first one it more difficult to develop and the third one very controversially resolves the issue you described.
   
- sequence details view:

   + wrap/unwrap sequence: the possibility to set by default a type (in one line or cut on several lines) should be included in preference because when you work on a DNA sequence with 6 translated frame it difficult to follow translation (maybe my brain is not designed for sequence on several lines).
This point is critical when you analyze dotplot with two sequences on the screen two follow for example DNA mutation and check if they are synonymous or not or affect DNA/RNA patterns.
---- The "Wrap mode" in sequence view already exists and there is a button to switch it on/off on the left part of the details vies.
   
- screens/windows: I have a reasonably sized screen (24 inches 16:9) with a second screen and I have difficulties see all sequence windows, especially if the main windows are a plasmid, a dotplot ...

suggestions:
   - the possibility to close the annotation view (fully)
---- https://ugene.dev/tracker/browse/UGENE-7207 - Make "Annotation Tree View" almost hidden with the splitter.

   - the possibility to order/move windows like sequence detail.. ,
---- We decided, that this feature is very controversial and won't be implemented.

  - is it not possible to have windows out of main ugene windows? (useful with several screens)
---- https://ugene.dev/tracker/browse/UGENE-7208 - Make possible to pull windows out of the UGENE window in the "Multiple documents" mode.
   
   
- Force In silico PCR:
It is possible to have degenerate primers for mutagenesis but it is not possible to force PCR (find product anyway) with primers with devoiding too much to dimers formation, Tm, GC%...

For example, is not possible to simulate direct mutagenesis with two overlapping primes (S /AS). Moreover, often we do not choose the region to amplify/mutate/sequence, and it could be GC deviant for example.
---- This isn't clear for me. Could you, please, provide more details about this feature?

Future?:

- Guide cloning/shRNA: We used synthetic hybrided oligos which not contain restriction sites but just cohesive end.
Maybe a tool to design a CRispR guide.

- recombinase cloning: it seems that it's an emerging technology, tools to design (and to virtual clone) could be useful

- R/bioconductor interaction (probably not trivial but will place Ugene at the level of G... ) ? : DEseq and proteomic (MS/MS analysis), improvement of data visualization?
---- About cloning - we already have some features we work on, it'll be a large update, but we still work on it.
 

Best regards,
Dmitrii Sukhomlinov,
UGENE team.
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Reply #2 - Jul 22nd, 2021 at 12:42am

ANTOINE   Offline
YaBB Newbies
France

Gender: male
Posts: 24
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Whaou !
I'm really impressed with how quickly you thought through the suggestions.
I apologize for my long silence and my late reaction but I had not seen your response.
I very happy for the suggestions that you take account.
I try to explain points clearly not clear:

1:- search in the project: the search is only on loaded data, I think that a search on unloaded should be great.
---- This feature has no sense since we get rid of the opportunity to unload objects from the project.
-> When I open a project all the sequences are unloaded. I can't use the search  to find a particular sequence. To find a sequence ( I have some projects with several (>50) sequences identify by GI), I must select all in the objects windows, right clic and load selected documents before search a specific sequence. It works but I don't no if is the correct way.

2- IUPAC code: In some sequences (mainly old) ambiguous nucleotides are annotaded for example N for any base, R for A or G,...
When in a sequence it appear a non atgc letter Ugene translate as X whatever the impact on translation: for example a CTN codon always give Leucine. As Ugene contain several codes IUPAC could be a plus.

3-  + wrap/unwrap sequence: the possibility to set by default a type (in one line or cut on several lines) should be included in preference because when you work on a DNA sequence with 6 translated frame it difficult to follow translation (maybe my brain is not designed for sequence on several lines).
This point is critical when you analyze dotplot with two sequences on the screen two follow for example DNA mutation and check if they are synonymous or not or affect DNA/RNA patterns.
---- The "Wrap mode" in sequence view already exists and there is a button to switch it on/off on the left part of the details vies.
-> By default the wrap mode is multi-line, I would have the possibility to select (in settings) the default mode to multi/singleline.

4- Force In silico PCR:
It is possible to have degenerate primers for mutagenesis but it is not possible to force PCR (find product anyway) with primers with devoiding too much to dimers formation, Tm, GC%...

For example, is not possible to simulate direct mutagenesis with two overlapping primes (S /AS). Moreover, often we do not choose the region to amplify/mutate/sequence, and it could be GC deviant for example.
---- This isn't clear for me. Could you, please, provide more details about this feature?

-> When certain parameters are not good: % GC, heterodimers,  Ugene does not give results. For example Ugene refuse to propose an amplification with a such primer : ATATAGTATGGGCAAGCA. When you work on HIV (~ 40% GC) you target often very poor GC sequences. 
Moreover, when you want amplify a circular DNA (mutagenesis, amplification of bacterial chromosomes, plasmids...), you use complementary primers. In these conditions Ugene or refuse to propose a amplification or only from short amplification corresponding to primers.
If you need more explanation I can prepare illustration.

Thanks a lot for your works and your reactivity.
Best regards,
Antoine


 
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