Plasmid Maps on Michael’s Domain

Opening old plasmid map files

Sat, 01 Jan 2022 00:00:00 +0000

For a new cloning project, we needed to access the plasmid maps of an old construct of mine (pSecTagN2, which was a precursor of pMosaic , aka pSecTagI) which I had composed from many different sources in 1999. In 1999, I was working in Kari Alitalo’s laboratory as a Ph.D. student. We were at the “cutting edge” of technology because we used a software program called Gene Construction Kit (GCK) to keep track of our clonings. Last Wednesday, I spent 4 hours of my working time opening one file created with GCK version 2.5 in 1999.

SnapGene - Simply the best DNA manipulation software

Fri, 01 Jan 2016 00:00:00 +0000

Our lab has been using different software packages to plan, document and visualize DNA constructs. Among those that we liked a lot for a long time were Textco’s GeneConstructionKit (GCK) and Clone Manager (Professional) . The latter runs unfortunately only under Windows. However, since several of our computers run Ubuntu Linux , we did run GCK versions 2.5 and 3 using WINE (a compatibility layer that allows us to run native Windows programs under Linux). However, with the upgrade to version 4, GCK became unusably slow under WINE and we were looking for a replacement. We contacted the developers of GCK, but they apparently were either not willing or able to help us. I suppose that the codebase of GCK is probably more than 20 years old and for that reason nobody dares to touch it. Just around that time, SnapGene was released and it fulfilled almost all of our requirements:

EMBOSS and GCK for the assembly and documentation of construct sequences

Thu, 05 Apr 2007 00:00:00 +0000

I am trying to use EMBOSS for the assembly of vector sequences. Long time ago, I used the CGC seqed program for this purpose and at the moment I use the Gene Construction Kit . EMBOSS doesn’t have a straight equivalent for seqed and one has to use a bunch of other tools to replace its functionality. Look at this comparison between CGC and EMBOSS .