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!

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.

You are welcome

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

You are welcome!

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).

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.