Computational nucleic acid coding and feature analysis
AssigneeMonsanto Technology LLC
InventorJames D. McIninch
Life of this patent
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Abstract
The present invention is in the field of bioinformatics, particularly as it pertains to gene prediction. More specifically, the invention relates to the probabilistic analysis of nucleic acid sequences for the determination of coding features, including determination of state probabilities for each nucleotide in a nucleic acid sequence, determination of coding strand, determination of open reading frame extent, determination of insertion and deletion location, determination of exon location, and determination of protein sequence.
Claims17
1-44. (Cancelled)
A method for determining a probability for one or more states for a selected nucleotide in a nucleic acid sequence, comprising:
- a) determining an initial oligonucleotide probability for each of said states for an initial oligonucleotide in said nucleic acid sequence;
- b) determining transition probabilities for each of said states for nucleotides within said nucleic acid sequence following said initial oligonucleotide;
- c) using said initial oligonucleotide probability and said transition probabilities to determine a plurality of nucleic acid sequence probabilities, said plurality comprising a nucleic acid sequence probability corresponding to each of said states for said selected nucleotide;
- and,
- d) applying a bias function to said plurality of nucleic acid sequence probabilities, to determine a probability for each of said states for said selected nucleotide, wherein said bias function does not have the same value in all of said states for said selected nucleotide.
A method for determining a probability for one or more states for a selected nucleotide in a nucleic acid sequence, comprising:
- a) determining an initial oligonucleotide probability for each of said states for an initial oligonucleotide in said nucleic acid sequence;
- b) determining transition probabilities for each of said states for nucleotides within said nucleic acid sequence following said initial oligonucleotide;
- c) using said initial oligonucleotide probability and said transition probabilities to determine a plurality of nucleic acid sequence probabilities, said plurality comprising a nucleic acid sequence probability corresponding to each of said states for said selected nucleotide;
- and,
- d) determining a probability for each of said states for said selected nucleotide, wherein said determining a probability for each of said states accepts a bias fiction, and wherein said bias function does not have the same value in all of said states for said selected nucleotide.
A method for determining a probability for each of one or more states for more than one selected nucleotide in a nucleic acid sequence comprising:
- a) determining an initial oligonucleotide probability for each of said states for an initial oligonucleotide in a window of a first selected nucleotide;
- b) determining transition probabilities for each of said states for nucleotides within said window following said initial oligonucleotide;
- c) using said initial oligonucleotide probability and said transition probabilities to determine a plurality of window probabilities, wherein said plurality comprises a window probability corresponding to each of said states for said selected nucleotide;
- d) applying a bias function to said plurality of window probabilities, to determine a probability for each of said states for said selected nucleotide, wherein said bias function does not have the same value in all of said states for said selected nucleotide;
- and,
- e) repeating steps a) through d) for each remaining selected nucleotide in said nucleic acid sequence.
Dependencies are inferred from the claim text.