US 8,014,955 B2Granted

Method of identifying unique target sequence

AssigneeGeorge Mason Intellectual Properties, Inc.

InventorsTariq Alsheddi, Anna Baranova

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Abstract

Described are methods and systems for designing target-specific oligonucleotides of L-length. The method comprises a) parsing a polynucleotide target into overlapping sequences of N-length nucleotides, creating a kernel set; b) performing step a) reiteratively for each target until each it is associated with its own kernel set; c) removing N-length kernels from the kernel sets which are redundant; d) concatenating X-length nucleotide suffixes to each N-length nucleotide kernel to create L-length oligonucleotide sets; e) ordering L-length nucleotides within each set of step d) by their nucleotide position within the target; f) retaining or rejecting an L-length oligonucleotide, based on the presence or absence of each of the X consecutive and overlapping N-length kernels; and g) performing step f) reiteratively. Step g) can be modified to parse L-length oligonucleotide sequences into overlapping Y-length nucleotides to create a set of Y-length kernels; and h) removing certain kernels that meet specified conditions.

Claims8

Dependent claims

A non-transient tangible computer readable medium containing computer readable instructions that when executed by one or more processors, cause the one or more processors to execute a method for designing a target-specific oligonucleotide sequence having an L-length in a polynucleotide population comprising polynucleotide targets, the method comprising:

a) exhaustively parsing a polynucleotide target into overlapping polynucleotide sequences of N-length nucleotides to create an N-length nucleotides kernel set for each target;
b) performing step a) reiteratively for each polynucleotide target that is a member of the polynucleotide population, until each polynucleotide target is associated with its own N-length nucleotide kernel set;
c) removing N-length nucleotide kernels from the N-length nucleotide kernel sets which are present in more than one N-length nucleotide kernel set;
d) choosing X-length nucleotide suffixes for each N-length nucleotide kernel, wherein the suffix consists of an X-length sequence of nucleotides that is upstream or downstream of the kernel, and optionally separated by a gap of nucleotides;
e) ordering L-length nucleotides consecutively within each set of step d) by their nucleotide position within the target polynucleotide, wherein each L-length nucleotide comprises consecutive and overlapping kernels;
f) 1) retaining an L-length oligonucleotide, if each of the X consecutive and overlapping N-length kernels are present after step e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix;
and
f) 2) rejecting an L-length oligonucleotide, if at least one of the X consecutive and overlapping N-length kernels is absent after steps e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix;
g) performing steps f)1 and f)2 reiteratively, beginning with the X+1 N-length kernel when all X-length suffixes are present;
or beginning with the kernel immediately following the absent suffix;
and
h) displaying the results of step (g) in a computer readable format to determine the identity of said target specific oligonucleotide sequence.

9 more elements

a) exhaustively parsing a polynucleotide target into overlapping polynucleotide sequences of N-length nucleotides to create an N-length nucleotide kernel set for each target;
b) performing step a) reiteratively for each polynucleotide target that is a member of the polynucleotide population, until each polynucleotide target is associated with its own N-length nucleotide kernel set;
c) removing N-length nucleotide kernels from the N-length nucleotide kernel sets which are present in more than one N-length nucleotide kernel set;
d) choosing X-length nucleotide suffixes for each N-length nucleotide kernel, wherein the suffix consists of an X-length sequence of nucleotides that is upstream or downstream of the kernel, and optionally separated by a gap of nucleotides;
e) ordering L-length nucleotides consecutively within each set of step d) by their nucleotide position within the target polynucleotide, wherein each L-length nucleotide comprises consecutive and overlapping kernels;
f) 1) retaining an L-length oligonucleotide if each of the X consecutive and overlapping N-length kernels are present after step e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix;
and
f) 2) rejecting an L-length oligonucleotide if at least one of the X consecutive and overlapping N-length kernels is absent after steps e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix;
g) exhaustively parsing L-length oligonucleotide sequences of step f) 1) into overlapping polynucleotide sequences of Y-length nucleotides to create a complete set of Y-length nucleotide kernels for each polynucleotide target, wherein each Y-length kernel comprises at least one nucleotide of the X-length nucleotide suffix;
and
h) removing Y-length nucleotide kernels from Y-length nucleotide kernel sets that meet at least one specified condition;
and
i) displaying the results of step (h) in a computer readable format to determine the identity of said target specific oligonucleotide sequence.

10 more elements

Dependencies are inferred from the claim text.

Facts

Application: 11/475,261Filed 27 Jun 2006 · us provisional application
Priority: 27 Jun 2005
Published: US 2007/0161012 A112 Jul 2007
Granted: 6 Sep 2011
Term ends: Not estimatedThe source records don’t support an estimate.

Classification3 codes

G16B 30/00
Ict specially adapted for sequence analysis involving nucleotides or amino acids
G16B 30/10
ICT specially adapted for sequence analysis involving nucleotides or amino acids: sequence alignment; Homology search
G16B
Bioinformatics, i.e. information and communication technology [ict] specially adapted for genetic or