Graphs for DNA Assembly
This web site contains research projects and results
on spatial graphs modeling DNA assembly.
The files in this site are work in progress
during 2009 - 2013, and will be updated often.
Any comments are welcome.
- Classification of assembly words and graphs
- Assembly numbers and polynomials
- Pathways of DNA recombination proceses via assembly graphs
- Nesting of assembly words and reductions
- Repeated pointer sequences in micronuclear genes
- Macronuclear segments in assembly graphs
- Planarity of assembly graphs
- Linking and writhe of assembly graphs
- Chirality of assembly graphs
Tables of assembly graphs for small numbers of rigid vertices
were obtained in 2009.
More extended table of assembly words were obtained by
Jonathan Burns in 2010.
Mathematica program are available here.
- The paper
``Polygonal Hamiltonian paths in regid 4-regular graphs and DNA assembly'',
contains the following results
obtained in 2010-2011.
- Number of isomorphism classes of assembly words
- Propserties of the assembly number
- Properties and computations of the assembly polynomial
- The number of Hamiltonian sets of polygonal paths
Poster by Natasha Jonoska at Frontiers in Mathematical Biology:
NSF-NIH PIs Meeting 2010.
Handout by Mary Billington
at the Undergraduate Research Symposium, USF, 2011
(winner of the top award `` Georg Kleine Award - Overall Best Oral Presentation'').
Workshop on discrete and topological methods in molecular biology
was held at USF in March 12-14, 2012, supported by NSF and USF.
These web sites are maintained by N. Jonoska and M. Saito,
with help from their collaborators and students.
This material is based upon work partially supported by
the National Science Foundation under Grant No. DMS-0900671.
Any opinions, findings, and conclusions or recommendations
expressed in this material are those of the author(s)
and do not necessarily reflect the views of the National Science Foundation.