US2006142951A1PendingUtilityA1
Computer software products for nucleic acid hybridization analysis
Est. expiryNov 22, 2020(expired)· nominal 20-yr term from priority
G16B 25/10G16B 25/00
65
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Claims
Abstract
Methods and computer software products are provided for analyzing gene expression data In one embodiment, multiple probes are used to detect a single transcript The hybridization intensities of each probe is adjusted by dividing the intensities by the affinities of the probes The minimal adjusted hybridization intensity may be used as the measurement of the gene expression
Claims
exact text as granted — not AI-modified1 . A computer implemented method for determining Hybridization between a plurality of nucleic acid probes and a nucleic acid target comprising
inputting a plurality of hybridization intensities, each of said intensities reflects said hybridization between one of said plurality of said probes and said nucleic acid target, adjusting said hybridization intensities for hybridization affinities of said probes to obtain a plurality of adjusted hybridization intensities, finding the minimal adjusted Hybridization intensity among said adjusted hybridization intensities; and indicating said minimal adjusted hybridization intensity as a measurement of said hybridization
2 . The method of claim 1 wherein said hybridization affinities of said probes are predicted based upon the sequence of said probes
3 . The method of claim 1 wherein said hybridization affinities are inputted from a database
4 . The method of claim 3 wherein said hybridization affinities are measured experimentally
5 . The method of claim 1 wherein said adjusted Hybridization intensity are calculated according to
Adjusted
hybridization
intensity
=
I
Γ
,
wherein said I is said Hybridization intensity and said Γ is said hybridization affinity
6 . The method of claim 5 wherein said plurality of probes have at least 5 probes
7 . The method of claim 6 wherein said plurality of probes have at least 10 probes
8 . The method of claim 7 wherein said plurality of probes have at least 20 probes
9 . A computer software product for determining hybridization between a plurality of nucleic acid probes and a nucleic acid target comprising
computer program code for inputting a plurality of Hybridization intensities, each of said hybridization intensities reflects said hybridization between one of said plurality of said probes and said nucleic acid target, computer program code for adjusting said hybridization intensities for hybridization affinities of said probes to obtain a plurality of adjusted hybridization intensities, computer program code for finding the minimal adjusted hybridization intensity among said adjusted hybridization intensities and computer program code for indicating said minimal adjusted hybridization intensity as a measurement of said hybridization, and a computer readable media for storing said code
10 . The computer software product of claim 9 wherein said hybridization affinities of
said probes are predicted based upon the sequence of said probes
11 . The computer software product of claim 10 wherein said Hybridization affinities inputted from a database
12 . The computer software product of claim 11 wherein said hybridization affinities are measured experimentally
13 . The computer software product of claim 12 wherein said adjusted Hybridization intensity are calculated according to.
Adjusted
hybridization
intensity
=
I
Γ
wherein said I is said hybridization intensity and said Γ is said hybridization affinity
14 . A computer-readable medium having computer-executable instructions for performing a method comprising,
inputting a plurality of hybridization intensities, each of said intensities reflects said hybridization between one of said plurality of said probes and said nucleic acid target, adjusting said hybridization intensities for hybridization affinities of said probes to obtain a plurality of adjusted hybridization intensities, finding the minimal adjusted hybridization intensity among said adjusted hybridization intensities, and indicating said minimal adjusted hybridization intensity as a measurement of said hybridization
15 . The computer readable medium of claim 14 wherein said hybridization affinities of said probes are predicted based upon the sequence of said probes
16 . The computer readable medium of claim 15 wherein said hybridization affinities are inputted from a database
17 . The computer readable medium of claim 16 wherein said hybridization affinities are measured experimentally
18 . The computer readable medium of claim 17 wherein said adjusted Hybridization intensity are calculated according to
Adjusted
hybridization
intensity
=
I
Γ
,
wherein said I is said hybridization intensity and said Γ is said hybridization affinity
19 . A system for comparing nucleic acid probes, comprising
a processor, and a memory being coupled to the processor, the memory storing a plurality machine instructions that cause the processor to perform a plurality of logical steps when implemented by the processor, said logical steps including
inputting a plurality of Hybridization intensities, each of said intensities reflects said hybridization between one of said plurality of said probes and said nucleic acid target,
adjusting said hybridization intensities for hybridization affinities of said probes to obtain a plurality of adjusted hybridization intensities,
finding the minimal adjusted hybridization intensity among said adjusted hybridization intensities, and
indicating said minimal adjusted hybridization intensity as a measurement of said hybridization
20 . The system of claim 19 wherein said hybridization affinities of said probes are predicted based upon the sequence of said probes
21 . The system of claim 20 wherein said hybridization affinities are inputted from a database
22 . The system of claim 21 wherein said hybridization affinities are measured experimentally
23 . The system of claim 22 wherein said adjusted hybridization intensity are calculated according to
Adjusted
hybridization
intensity
=
I
Γ
,
wherein said I is said hybridization intensity and said Γ is said hybridization affinityJoin the waitlist — get patent alerts
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