Dnastar, Inc.

Schuyler F Baldwin

Frederick R Blattner

Daniel A Nash

Richard D Nelson

Timothy J Durfee

Kenneth C Dullea

Tim Durfee

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

Systems and methods automatically identify a set of read sequences in one or more larger nucleotide sequences within a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to identify matches of the read sequence set in one or more larger nucleotide sequence databases.

Systems and methods for identifying nucleotide sequence matches

Systems and methods automatically assemble a set of read sequences into one or more larger nucleotide sequences using a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to assemble the read sequence set into one or more larger nucleotide sequences.

System for assembling a derived nucleotide sequence

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Madison, WI, United States of America

Schuyler F Baldwin