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WO1999066302A3 - Recognition of protein coding regions in genomic dna sequences - Google Patents

Recognition of protein coding regions in genomic dna sequences Download PDF

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Publication number
WO1999066302A3
WO1999066302A3 PCT/US1999/013705 US9913705W WO9966302A3 WO 1999066302 A3 WO1999066302 A3 WO 1999066302A3 US 9913705 W US9913705 W US 9913705W WO 9966302 A3 WO9966302 A3 WO 9966302A3
Authority
WO
WIPO (PCT)
Prior art keywords
coding
nucleotide position
dna sequence
nucleotide
sensor
Prior art date
Application number
PCT/US1999/013705
Other languages
French (fr)
Other versions
WO1999066302A9 (en
WO1999066302A2 (en
Inventor
Yuandan Lou
Zhen Zhang
Original Assignee
Musc Found For Res Dev
Yuandan Lou
Zhen Zhang
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Musc Found For Res Dev, Yuandan Lou, Zhen Zhang filed Critical Musc Found For Res Dev
Priority to AU46917/99A priority Critical patent/AU4691799A/en
Publication of WO1999066302A2 publication Critical patent/WO1999066302A2/en
Publication of WO1999066302A3 publication Critical patent/WO1999066302A3/en
Publication of WO1999066302A9 publication Critical patent/WO1999066302A9/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

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  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Analytical Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Biomedical Technology (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Molecular Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A coding sensor using a recurrent neural network technique is provided. The coding sensor indicates the coding potential of a gene sequence and plays a vital role in the overall prediction of the gene structure. The recognition of the potential coding regions in a DNA sequence may be achieved by determining whether each individual nucleotide position in a nucleotide chain is in a coding region. Determining whether an individual nucleotide position is in a coding region may be accomplished through a systematic sampling process carried out along the nucleotide chain from start to end. The content variables of neighboring nucleotide positions are processed using a trained recurrent neural network in order to provide a coding sensor value. In this way, transition characteristics may be used to assist the coding sensor in determining whether a nucleotide position is in a coding region. The coding sensor value represents a prediction of whether or not the nucleotide position is in a coding region. Coding sensor values for each nucleotide position in the DNA sequence are aligned with the overall DNA sequence to generate a coding/non-coding picture of the DNA sequence.
PCT/US1999/013705 1998-06-17 1999-06-17 Recognition of protein coding regions in genomic dna sequences WO1999066302A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU46917/99A AU4691799A (en) 1998-06-17 1999-06-17 Recognition of protein coding regions in genomic dna sequences

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US8968098P 1998-06-17 1998-06-17
US60/089,680 1998-06-17

Publications (3)

Publication Number Publication Date
WO1999066302A2 WO1999066302A2 (en) 1999-12-23
WO1999066302A3 true WO1999066302A3 (en) 2000-06-22
WO1999066302A9 WO1999066302A9 (en) 2000-07-27

Family

ID=22219015

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/013705 WO1999066302A2 (en) 1998-06-17 1999-06-17 Recognition of protein coding regions in genomic dna sequences

Country Status (2)

Country Link
AU (1) AU4691799A (en)
WO (1) WO1999066302A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030190603A1 (en) * 2000-06-08 2003-10-09 Brendan Larder Method and system for predicting therapeutic agent resistance and for defining the genetic basis of drug resistance using neural networks
US7158889B2 (en) 2002-12-20 2007-01-02 International Business Machines Corporation Gene finding using ordered sets
US10957421B2 (en) 2014-12-03 2021-03-23 Syracuse University System and method for inter-species DNA mixture interpretation
CN111370055B (en) * 2020-03-05 2023-05-23 中南大学 Method for establishing intron retention prediction model and its prediction method
CA3190092A1 (en) 2020-08-21 2022-02-24 Felix MUERDTER Methods and systems for sequence generation and prediction
CN113808671B (en) * 2021-08-30 2024-02-06 西安理工大学 Method for distinguishing coding ribonucleic acid from non-coding ribonucleic acid based on deep learning
CN117745704B (en) * 2023-09-27 2025-02-25 深圳泰康医疗设备有限公司 A spinal region segmentation system for osteoporosis identification

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
SNYDER ET AL.: "Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks", NUCLEIC ACIDS RESEARCH,, vol. 21, no. 3, 1993, pages 607 - 613, XP002925273 *
SNYDER ET AL.: "Identification of Protein Coding Regions in Genomic DNA", JOURNAL OF MOLECULAR BIOLOGY,, vol. 248, 1995, pages 1 - 18, XP002925271 *
UBERBACHER ET AL.: "Locating protein-encoding regions in human DNA sequence by a multiple sensor-neural network approach", PROC. NATL. ACAD. SCI. USA,, vol. 88, December 1991 (1991-12-01), pages 11261 - 11265, XP002925272 *

Also Published As

Publication number Publication date
WO1999066302A9 (en) 2000-07-27
WO1999066302A2 (en) 1999-12-23
AU4691799A (en) 2000-01-05

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