DNA sequence similarity recognition by hybridization to short oligomers

Milosavljevic, Aleksandar

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Title: DNA sequence similarity recognition by hybridization to short oligomers

Abstract

Methods are disclosed for the comparison of nucleic acid sequences. Data is generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated is manipulated simultaneously with respect to both (i) matching between oligomers and (ii) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.

Inventors:

Milosavljevic, Aleksandar ^[1]

Westmont, IL

Issue Date:: Fri Jan 01 00:00:00 EST 1999

Research Org.:: Argonne National Laboratory (ANL), Argonne, IL (United States)

OSTI Identifier:: 872753

Patent Number(s):: 6001562

Assignee:: University of Chicago (Argonne, IL)

Patent Classifications (CPCs):: C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/6874 - involving nucleic acid arrays, e.g. sequencing by hybridisation

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DOE Contract Number:: W-31109-ENG-38

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: dna; sequence; similarity; recognition; hybridization; oligomers; methods; disclosed; comparison; nucleic; acid; sequences; data; generated; hybridizing; sets; target; acids; manipulated; simultaneously; respect; matching; ii; putative; reference; available; databases; compression; manipulate; mutual; information; constructed; compression methods; data compression; reference sequence; dna sequence; acid sequence; nucleic acid; acid sequences; nucleic acids; target nucleic; reference sequences; target nuclei; /435/999/

Citation Formats


                    Milosavljevic, Aleksandar. DNA sequence similarity recognition by hybridization to short oligomers.  United States: N. p., 1999. 
        Web.

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                    Milosavljevic, Aleksandar. DNA sequence similarity recognition by hybridization to short oligomers.  United States.

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                    Milosavljevic, Aleksandar. Fri .  
        "DNA sequence similarity recognition by hybridization to short oligomers".  United States.  https://www.osti.gov/servlets/purl/872753.

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@article{osti_872753,

  title        = {DNA sequence similarity recognition by hybridization to short oligomers},

  author       = {Milosavljevic, Aleksandar},

  abstractNote = {Methods are disclosed for the comparison of nucleic acid sequences. Data is generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated is manipulated simultaneously with respect to both (i) matching between oligomers and (ii) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {Fri Jan 01 00:00:00 EST 1999},

  month        = {Fri Jan 01 00:00:00 EST 1999}

}

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Works referenced in this record:

Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes
journal, January 1992

Drmanac, Radoje; Drmanac, Snezana; Labat, Ivan
Electrophoresis, Vol. 13, Issue 1
https://doi.org/10.1002/elps.11501301115

Hybridization analyses of arrayed cDNA libraries
journal, October 1991

Lennon, Gregory G.; Lehrach, Hans
Trends in Genetics, Vol. 7, Issue 10
https://doi.org/10.1016/0168-9525(91)90420-U

Biological Evaluation of d ² , an Algorithm for High-Performance Sequence Comparison
journal, January 1994

Hide, Winston; Burke, John; Da Vison, Daniel B.
Journal of Computational Biology, Vol. 1, Issue 3
https://doi.org/10.1089/cmb.1994.1.199

Statistical distance between texts and filtration methods in sequence comparison
journal, January 1992

Pevzner, Pavel A.
Bioinformatics, Vol. 8, Issue 2
https://doi.org/10.1093/bioinformatics/8.2.121

Discovering simple DNA sequences by the algorithmic significance method
journal, January 1993

Milosavljević, Aleksandar; Jurka, Jerzy
Bioinformatics, Vol. 9, Issue 4
https://doi.org/10.1093/bioinformatics/9.4.407

Mathematical Foundations of Computer Science 1994
book, January 1994

Prívara, Igor; Rovan, Branislav; Ruzička, Peter
Lecture Notes in Computer Science
https://doi.org/10.1007/3-540-58338-6

Systematic sequencing of the Escherichia coli genome: analysis of the 0 – 2.4 min region
journal, January 1992

Yura, Takashi; Mori, Hirotada; Nagai, Hiroki
Nucleic Acids Research, Vol. 20, Issue 13
https://doi.org/10.1093/nar/20.13.3305

1-Tuple DNA Sequencing: Computer Analysis
journal, August 1989

Pevzner, Pavel A.
Journal of Biomolecular Structure and Dynamics, Vol. 7, Issue 1
https://doi.org/10.1080/07391102.1989.10507752

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DNA sequence similarity recognition by hybridization to short oligomers

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Methods are disclosed for the comparison of nucleic acid sequences. Data are generated by hybridizing sets of oligomers with target nucleic acids. The data thus generated are manipulated simultaneously with respect to both (1) matching between oligomers and (2) matching between oligomers and putative reference sequences available in databases. Using data compression methods to manipulate this mutual information, sequences for the target can be constructed.
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A newly developed method for sequence recognition by hybridization to short oligomers is verified for the first time in genome-scale experiments. The experiments involved hybridization of 15,328 randomly selected 2-kb genomic clones of Escherichia coli with 997 short oligomer probes to detect complementary oligomers within the clones. Lists of oligomers detected within individual clones were compiled into a database. The database was then searched using known E. coli sequences as queries. The goal was to recognize the clones that are identical or similar to the query sequences. A total of 76 putative recognitions were tested in two separate but complementarymore » « less
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Recently developed hybridization technology enables economical large-scale detection of short oligomers within DNA fragments. The newly developed recognition method enables comparison of lists of oligomers detected within DNA fragments against known DNA sequences. We here describe an experiment involving a set of 4513 distinct genomic E. coli clones of average length 2kb, each hybridized with 636 randomly selected short oligomer probes. High hybridization signal with a particular probe was used as an indication of the presence of a complementary oligomer in the particular clone. For each clone, a list of oligomers with highest hybridization signals was compiled. The database consistingmore » « less
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Full Text Available

Similar Records

Title: DNA sequence similarity recognition by hybridization to short oligomers

Abstract

Citation Formats

Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes journal, January 1992

Hybridization analyses of arrayed cDNA libraries journal, October 1991

Biological Evaluation of d 2 , an Algorithm for High-Performance Sequence Comparison journal, January 1994

Statistical distance between texts and filtration methods in sequence comparison journal, January 1992

Discovering simple DNA sequences by the algorithmic significance method journal, January 1993

Mathematical Foundations of Computer Science 1994 book, January 1994

Systematic sequencing of the Escherichia coli genome: analysis of the 0 – 2.4 min region journal, January 1992

1-Tuple DNA Sequencing: Computer Analysis journal, August 1989

Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes
journal, January 1992

Hybridization analyses of arrayed cDNA libraries
journal, October 1991

Biological Evaluation of d ² , an Algorithm for High-Performance Sequence Comparison
journal, January 1994

Statistical distance between texts and filtration methods in sequence comparison
journal, January 1992

Discovering simple DNA sequences by the algorithmic significance method
journal, January 1993

Mathematical Foundations of Computer Science 1994
book, January 1994

Systematic sequencing of the Escherichia coli genome: analysis of the 0 – 2.4 min region
journal, January 1992

1-Tuple DNA Sequencing: Computer Analysis
journal, August 1989