Hi guys I have just checked out Ugene and it seems quite impressive (although I am on an old version because it was the only one I could find in the opensuse repositories).

I think a nice feature would be some sort of meta-plugin (annotation+RE site finder) and a circular DNA viewer for familiar looking cloning (sequence selection by RE, ligation). Perhaps even a point-and-click cloning interface, which basically acts as a GUI front end for editing genbank files.

Basically what I am suggesting is a plug-in that could act as a replacement for vector NTI and similar programs :).
I am not sure if it would be possible to pull code from GENtle for this...

Hi Jens
Circular DNA viewer + cloning functionality have always been in our plans. We will consider inluding it in UGENE 1.7 (release is scheduled to the end of 2009).

BTW, you can try download and install fedora RPM - there must be no problems using it.
Thanks for your interest in UGENE!

Hi

Thanks for that answer :) I will be very happy when that functionality is added :).

Installing the fedora RPM (11_64) on OpenSuse (11.2/Factory_64) was a bad idea unfortunately.

The 1.3.3 version available via the opensuse repositories ran but the 1.5 version via Fedora RPM crashes with a segmentation error output (row 4 of /usr/lib64/ugene/ugene $*) every time...

I will try a bit more and if I figure out what is wrong, I will report back about it :)

Well, I can suggest you the following:
1) before installing 1.5 rpm, the old one must be completely removed.
2) ensure that you have a proper Qt version: 4.5.1 or later.

I think we will try to provide Suse support for the upcoming release. :)

Thanks for the tips. After downgrading to the previous package and then removing it, I could install the Fedora package on OpenSuse. So in fact you are already supporting it :)

Thanks for a great program. I will try to invest some time in learning it and recommending it to others - and I look forward to version 1.7 and its cloning plugin (my institute is currently addicted to VectorNTI which is insanely expensive).

You are welcome :)

Hi sorry to bother again

I tried installing the 1.6 in 3 different ways on my 64-bit opensuse 11.2

First, the fedora RPM complains about not having qt>4.5, which is false. I have 4.6. Second it complains about not having qt-x11, which also is false. Can this compatibility be solved using symlinks so that the rpm can find the required dependencies?

The second strategy was the install script for suse in the tarball. This also failed on the initial step, where it checks:
if ! uname -a | grep -i "opensuse" >/dev/null 2>&1;

(no string "opensuse" after uname only kernel version etc)

The third strategy was compiling it using
qmake CONFIG+=x64 -r

This worked a bit better (after long compilation with  some warnings)
starting ugene does however not work because it can not find proper translation for my system (which I do not have any interest in). Is there a way to disable the translation check and/or set to default English?

Hi Jens,
thanks for the report. We will fix the issue with broken qt dependencies and check if translations on SuSE are generated properly.

For now, I can suggest you a quick-and-dirty solution:

1) Translations are binary files called transl_en.qm and transl_ru.qm which must be generated during the UGENE build. UGENE cannot start if no translation files are located nearby its binary.

So, the solution is:
- try to generate translations by hand. Just run qmake in the root dir of the source package and check directory src/_release. Translation files should be generated here.
- copy translation files (e.g. transl_en.qm) to the directory where ugene binary is placed (e. g. /usr/lib/ugene)

In case of problems please provide the following info:
- logs of qmake
- way you use to start ugene

Copying the translation file to /usr/lib/ugene worked nicely! Thanks!

The way I start it is by executing the "ugene" start script file generated during make (the one exporting a path to /usr/lib/ugene and then starts ugene).

I am not very used to compile my own programs but it seems to have worked :)

You are welcome!

thanks for this feature.
will test it as soon i got the 1.6.2 ubuntu package running.

i just started playing around with serial cloner, gentle and pdraw - but this may not be needed now. one more programm windows isn´t needed for.  ;D

Hi,

is the "cloning" plugin already fully integrated? I don't want to sound rude - ugene is a very nice software - may-be I'm just blind  :) but i've just found RE-analysis. I'm also looking for features like pcr- (with clonig-primer-design), restriction-, ligation- and virtual-gel-simulation and so on (features you can find in software like Serial Cloner or GENtle).

Sebastian,
some of the features like, for example, circular view, are already integrated.
We're planning to continue working on it.

To implement such big task as cloning we need to break it into smaller parts, thus it would be nice of you to provide some "real-life" scenario of "cloning" process with basic steps  :)  
This will help us to concentrate our efforts on the most important features.

Konstantin,

thank you for your reply. I'm new to ugene, so i was just wondering.
To your request:

One typical task/workflow to test a cloning strategy in silico for me:

I have vector A with insert 1 and vector B with a MCS or insert 2 and after cloning i want to have Vector B with insert 1.

1. Find RE-sites in both vectors witch extract the insert 1 and "opens" vector 2.

2. If no compatible RE-sites are present simulate PCR to add RE-sites to insert 1 - a cloning Primer design and analysis tool would be great. This tool should generate a primer pair at the ends of a selected region and insert features like RE-sites via additional miss matching regions. Check for hairpin, primer dimers, melting temperature etc.

3. virtually cut vectors/pcr product - would be nice if you could just select an RE combination for example in circular view or linear view in case of PCR product an directly extract the selected sequences into a new ones (with overhangs after cut).

4. virtually ligate the two linear DNA-sequences (optional: should be possible to add a 3rd DNA sequence) - this feature should check if DNA ends are compatible (overhangs) and provide an option for "blunting" of potential sticky ends and generate a new sequence after ligation.

All steps should conserve annotations from template vectors/inserts and in case of "disruption" of an annotated sequence by RE cut the user should be warned.

The main reasons why i use such features:

1. Find a suitable cloning strategy
2. Control if I really get the desired vector and insert combination (no frame shifts etc.)
3. Always have an up-to-date sequence and map of my vectors (I usually check the insert-region by sequencing afterwards and align the theoretical sequence against the detected)

May-be it helps if you take a look at GENtle. It's a software released under GPL that provides most of the features.

In addition to those features that Sebastian suggested in the earlier message, I often do cloning projects in vectors designed to make fusion proteins. For example the vector pGEX4T-1 makes glutathione-S-transferase (GST). The ORF search in UGene allows you to check and see what kind of fusion protein is made after cloning into GST, but the steps to do the conceptual translation and to check the identity of the different parts of the fusion protein could be smoother. In particular, when planning an experiment like this, you need to be sure that the gene segment inserted is in frame with the protein in the vector so the proper fusion protein is synthesized.

Although there is not a cloning plugin as such, I was able to do part of what was requested by using the "remove subsequence" and "add subsequence" options under "Edit Sequence". Thanks again with the help on this, by the way.

JohnR

Sebastian, John,
thanks for the suggestions and detailed explanation!

We are planning to improve cloning pipeline in version 1.7.2 ( scheduled for September 2010) and further releases. Stay tuned for UGENE updates.

Thank you very much for fixing the bug I reported a few days ago (http://ugene.unipro.ru/forum/YaBB.pl?num=1296858562) so fast. It' s working fine now. Additionally I have two suggestions for you which would in my opinion simplify the working with the cloning pipeline.
1. Since the widely used expression vectors of the pET system (Novagen, http://www.emdchemicals.com/life-science-research/pet/c_2tOb.s1OkacAAAEjWhl9.zLX) are numbered by the pBR322 convention (the T7 expression region is reversed on the
circular map) it would be nice to be able to reverse complement a fragment during cloning (without first creating a new molecule in Ugene). Maybe you could add an option like "Reverse complement Fragment" or "Invert fragment" in the "Edit molecule fragment" dialog of the cloning pipeline.
2. Since you are sometimes cloning PCR fragments into a blunt end cutted vector, it may be useful to be able to add DNA molecules from the current Ugene project into the cloning pipeline. Maybe you could add an option like "Add molecule from current project" to the "construct molecule" dialog. Due to clarity, I would not suggest to add all molecules to the "Available fragments" selection by default.
Thank you again for Ugene.
Best regards

These two suggestions are interesting features indeed, especially the second one: adding molecule from project and refering to it as a fragment. I suppose nice implementation will be a "fragment manager" - container of fragments for active project with possible options to create new fragments: import documents from project, PCR amplication, etc.
However the first implementation most likely will be, as you suggested, option for import project documents in "Construct Molecule" dialog.

We will put these features on our TODO list for 1.9.2.

Peacemaker wrote on Feb 9^th, 2011 at 1:50pm:

... Additionally I have two suggestions for you which would in my opinion simplify the working with the cloning pipeline. 1. Since the widely used expression vectors of the pET system (Novagen, http://www.emdchemicals.com/life-science-research/pet/c_2tOb.s1OkacAAAEjWhl9.zLX) are numbered by the pBR322 convention (the T7 expression region is reversed on the circular map) it would be nice to be able to reverse complement a fragment during cloning (without first creating a new molecule in Ugene). Maybe you could add an option like "Reverse complement Fragment" or "Invert fragment" in the "Edit molecule fragment" dialog of the cloning pipeline. 2. Since you are sometimes cloning PCR fragments into a blunt end cutted vector, it may be useful to be able to add DNA molecules from the current Ugene project into the cloning pipeline. Maybe you could add an option like "Add molecule from current project" to the "construct molecule" dialog. Due to clarity, I would not suggest to add all molecules to the "Available fragments" selection by default.

Good news! The suggested features are implemented and available via latest snapshot. Check attached screenshot for quick help.

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