Does Clotho enable a user to store basic parts and construct intermediates in a database, then run a search for constructs that will enable the fastest assembly of a larger construct? For instance, if I have A, B, C, D, AB, CA, and ABD in my collection, and want to build CABD, can I use Clotho to quickly determine that C + ABD is the fastest assembly strategy?

This would be useful for parsing my 300+ parts and constructs. I’ve been trying to find a DNA parts tool with this feature to no avail.

Thanks!

Karmella,

Thanks for the question and starting to participate!

First of all, Clotho does allow you to store basic parts as well as composite parts.

As for determining optimal assemblies based on that information, Clotho 2.0 does not have an App for that yet (as of 11/10/10). Although since the information is there, you could write your own App for this (although I am guessing you don’t want to get that involved yet).

Older versions of Clotho had assembly programs in them but they have not been ported over yet. I am working on doing so now. It should be available sometime in January. The assembly algorithm to be ported first will be based on:

Douglas Densmore, Timothy H.-C. Hsiau, Joshua T. Kittleson, Will DeLoache, Christopher Batten, J.Christopher Anderson,
Algorithms for Automated DNA Assembly, Nucleic Acids Research (2010) 38 (8): 2607-2616. PMID: 20335162

This does exactly what you are talking about.

If you are interested in checking out the older versions of Clotho to see how it worked let me (us) know and we can provide more instructions. The biggest issue is that the old algorithms are not connected to a database so they won’t be able to use knowledge about your “part library”.

Also, since I am close to Harvard, I would be happy to visit with you more if you like,

Doug

Hi Doug. Thanks for your fast response. I will go ahead and start adding DNA parts to the recent version of Clotho to try it out. I’m big on organization and like the direction Clotho is heading. As long as the parts are searchable, that will be of immediate use for my work.

Congrats on the recent paper! Will was on the Davidson iGEM team when I was there as a postdoc advisor.

Best,
—-Karmella

Karmella,

Great! Please do use Clotho and let us know what you think. Questions and comments are always welcome. We are constantly improving things and probably will have another version out with more features and functionality by the end of the year.

Doug