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1. (US20170053061) METHOD AND SYSTEM FOR MULTIPLEX PRIMER DESIGN

Office : United States of America
Application Number: 15240919 Application Date: 18.08.2016
Publication Number: 20170053061 Publication Date: 23.02.2017
Publication Kind : A1
IPC:
G06F 19/20
C12Q 1/68
G01N 35/00
G06F 19/22
C40B 30/02
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
20
for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
Q
MEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1
Measuring or testing processes involving enzymes or micro-organisms; Compositions therefor; Processes of preparing such compositions
68
involving nucleic acids
G PHYSICS
01
MEASURING; TESTING
N
INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
35
Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/-G01N33/148; Handling materials therefor
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22
for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
30
Methods of screening libraries
02
In silico screening
CPC:
G06F 19/20
G06F 19/22
C40B 30/02
G01N 35/0099
C12Q 1/6844
Applicants: uBiome, Inc.
Inventors: Daniel Almonacid
Zachary Apte
Jessica Richman
Priority Data:
Title: (EN) METHOD AND SYSTEM FOR MULTIPLEX PRIMER DESIGN
Abstract: front page image
(EN)

A method and system for selection of a primer set for a set of target sequences includes: identifying candidate fragments upon performance of a comparison operation with the set of target sequences; identifying a forward subset of unique forward candidates and a reverse subset of unique reverse candidates; reducing the forward subset and the reverse subset based on a filtering operation; performing an in silico search operation with the reduced forward subset and the reduced reverse subset; generating a set of candidate degenerate primers based on the in silico search operation and a base mismatch criterion; generating a reduced set of candidate degenerate primers upon filtering the set of candidate degenerate primers according to the set of primer criteria; and selecting forward primer subsets that amplify the set of target sequences and identifying a reverse primer subset for each of the forward primer subsets with an in silico PCR operation.