Hi to everyone,
I am a molecular biologist and have been useing Ugene for about 3 years now. My applications were mainly plasmid-based, like restriction analysis, molecular cloning, PCR, Gibbson Assembly.
I liked the open source philosophy of Ugene and although many things in Ugene are great, there are other basic things, which a molecular biologist needs, that are missing. I thougt that these problems would be solved with time and I therefor posted my suggestions here in the forum.
However these suggestions are more than a year old now and nothing has happend since. Mainly:
- If a sequence is circular or linear is a physical property of the sequence and should be attached to it like an attribute. This is the only way that makes sense in my opinion. In Ugene however, whether the sequence is circular or not has to be selected when a tool is applied to the sequence, like restriction analysis or restriction digestion. For other tools there is no such option at all. For example you can not select a subsequence from a plasmid that contains the start/end point. If you select from 4000 bp to 1000 bp in the "select sequence region" tool, nothing happens. Also there is no option for circular molecules in the basic search tool or the smith-waterman algorithm. So if the search pattern is in the sequence, but by chance contains the start/end point, it is not found. In my opinion this is simply abominable. Here are the links to the forum postes which I refer to:
http://ugene.unipro.ru/forum/YaBB.pl?num=1355062671
http://ugene.unipro.ru/forum/YaBB.pl?num=1369910696

- Also there are still no tools for PCR or Gibbson Assembly planning. The idea for a PCR tool is around since 2011 and to my impression nothing has happend since ( see https://ugene.unipro.ru/tracker/browse/UGENE-256)

I understand the problems associated with a free software project and do not know how much efforts you developers still can or want to put into the project. So I don't want to complain and just tell you my opinion on behalf of the usefulness of Ugene for molecular biologists.

Conceptually I also have the impression, that ugene has two types of users in mind, which make it kind of a hybrid. On the one hand are the molecular biologists, who want to plan their daily lab experiments with Ugene. They work with Plasmids ans short sequences and want to simulate PCR, restriction digestion, ligation, ... (molecular biology stuff). On the other hand Ugene is also made for more complex bioinformatical applications like analysis of whole bacterial genomes, contig assembly, etc.
Considering that there were no major improvements made for the molecular biology field in the last time, I have the impression that you, the developers, rather focus on the bioinformatics applications. I think this is a good idea, but it has to be made clear than, that Ugene is only partly useful for molecular biologists.

Thanks you for letting me express my ideas about the Ugene project.

Cheers,
Thomas

I'd like to second Randolf's comments, I think LIC cloning now represents about 90% of the cloning we do, so implementing this in Ugene would be a great asset, but of course must fit in with your current coding priorities.