The United States of America as Represented by the Department of Energy

Dnastar, Inc.

Tim Durfee

Wilhelm Gruissem

Judith L Roe

Heidi Feiler

Susan Jenkins

Patricia Zambryski

Frederick R Blattner

Schuyler F Baldwin

Daniel A Nash

Madalina Miskoski

Systems and methods to automatically de novo assemble a set of unordered read sequences into one or more, larger nucleotide sequences are presented. The method involves first creating two identical sets of the reads, dividing each read in both sets into smaller sorted mer sequences and then comparing the mers for each read in set 1 to the mers from each read in set 2 to exhaustively identify overlapping segments. Overlap information is used to construct a modified assembly string graph, traversal of which produces a sorted string graph layout file consisting of all the reads ordered left to right including their approximate starting offset position. The sorted string graph layout file is then processed by a novel multiple sequence alignment system that uses mer matches between all the overlapping reads at a given position to place matching individual bases from each read into columns from which an overall consensus sequence is determined.

Systems and methods for de novo assembly of nucleotide sequence reads using a modified string graph

This invention provides methods and compositions for altering the growth, organization, and differentiation of plant tissues. The invention is based on the discovery that, in plants, genetically altering the levels of Retinoblastoma-related gene (RRB) activity produces dramatic effects on the growth, proliferation, organization, and differentiation of plant meristem.

Alteration of plant meristem function by manipulation of the Retinoblastoma-like plant RRB gene

Retinoblastoma-like RRB gene of arabidopsis thaliana

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Madison, WI, United States of America

Tim Durfee