Research Group, Summer 2011

This web site contains research projects, materials, and summary of findings
on spatial graphs modeling DNA assembly for the reaserch group of Summer 2011.

Projects

• Patheways of DNA recombination precesses via assembly graphs
• Nesting of assembly words
• Repeated poiners in micronuclear genes
• Macronuclear segments in assembly graphs and words

Findings

• Reduction and Nexting Indices of Double Occurrence Words by Ryan Arredondo (continued to Class of 2011)
• Micronuclear Sequences Associated with Assembly Graphs by Christeen Bisnath
• Unscrambling of the Actin I gene in Micronuclear Rearrangements by Maja Milosevic
• Pointer Sequence Positions in Macronuclear Destined Sequences by Tim Yeatman

Material used for Projects: DNA Sequences of Ciliates

The following information was downloaded from
http://oxytricha.princeton.edu/dimorphism .

• Sterkiella nova Actin I gene
  This is a gene used to model its assembly by an assembly graph for the first time.
  Info, Sequence.
• Stylonychia pustulata Actin I gene
  This is the only one for which all pathways are known and connected.
  Info, Sequence.
• Sterkiella histriomuscorum Actin I gene
  Trifallax, this contains disconnected components in pathways.
  Info, Sequence.
• Sterkiella histriomuscorum DNA Polymerase Alpha gene
  This is one of the largest known.
  Info, Sequence.

In the table at http://oxytricha.princeton.edu/dimorphism;
Unscrambled genes (with conventional IESs) are:
3, 35, 2, 40, 13, 31, 4, 34, 24, 16, 15, 30, 43, 29, 10, 9, 5.
Scrambled ones (with permutations or inversions) are:
38, 1, 28, 32, 42, 41, 37, 33, 44, 19, 26, 36.

Group Members of Summer 2011

• Undergraduate: Ryan Arredondo, Christeen Bisnath, Maja Milosevic, Timothy Yeatman.
• Graduate: Jonathan Burns, Egor Dolzhenko, Tilahun Muche.

People

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.