Method and apparatus for analyzing nucleic acid sequences

A computer program product comprising computer-readable media having computer-readable code which, when run on a computer, causes the computer to analyze a nucleic acid sequence based on a set of nucleic acid sequence data, the computer program product comprising the following computer-readable program code for effecting actions in the computer:

• program code for identifying, based on the nucleic acid sequence data, each open reading frame (ORF) of the nucleic acid sequence;
• program code for calculating a score for each identified ORF of the nucleic acid sequence, wherein said calculating comprises examining the periodicity of each base in each identified ORF at a frequency of ⅓;
• program code for comparing the calculated score of each ORF to a predetermined threshold and for determining whether the score of the ORF is greater than or equal to the predetermined threshold;
• and
• program code for identifying a probable coding region in the nucleic acid sequence based on the score of each ORF that is determined to be greater than or equal to the predetermined threshold.

A computer program product comprising computer-readable media having computer-readable code which, when run on a computer, causes the computer to analyze a nucleic acid sequence based on a set of sequence data, the computer program product comprising the following computer-readable program code for effecting actions in the computer:

• program code for identifying, based on the nucleic acid sequence data, predetermined regions of the nucleic acid sequence;
• program code for calculating a score for each identified region of the nucleic acid sequence, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓;
• program code for comparing the calculated score of each region to a predetermined threshold;
• and
• program code for identifying a probable coding region in the nucleic acid sequence based on the comparison of the score of each region to the predetermined threshold,
• wherein said program code for identifying a coding region comprises program code for identifying each open reading frame (ORF) having a score greater than or equal to the predetermined threshold as corresponding to a probable coding region.

A computer program product comprising computer-readable media having computer-readable code which, when run on a computer, causes the computer to analyze a nucleic acid sequence based on a set of sequence data, the computer program product comprising the following computer-readable program code for effecting actions in the computer:

• program code for identifying predetermined regions of the nucleic acid sequence based on the sequence data;
• program code for calculating a score for each identified region of the nucleic acid sequence, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓;
• program code for comparing the calculated score of each region to a predetermined threshold;
• and
• program code for identifying a probable coding region in the nucleic acid sequence based on the comparison of the score of each region to the predetermined threshold,
• wherein said program code for identifying predetermined regions comprises program code for locating each region of the nucleic acid sequence that is between pairs of in-frame termination codons.

A computer program comprising computer-readable media having computer-readable code which, when run on a computer, causes the computer to analyze a nucleic acid sequence based on a set of sequence data, the computer program product comprising the following computer-readable program code for effecting actions in the computer:

• program code for identifying predetermined regions of the nucleic acid sequence based on the sequence data;
• program code for calculating a score for each identified region of the nucleic acid sequence, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓;
• program code for comparing the calculated score of each region to a predetermined threshold;
• and
• program code for identifying a probable coding region in the nucleic acid sequence based on the comparison of the score of each region to the predetermined threshold,
• wherein said program code for identifying predetermined regions comprises program code for locating each region of the nucleic acid sequence that is between an initiation codon and an in-frame termination codon.

A computer program product comprising computer-readable media having computer-readable code which, when run on a computer, causes the computer to analyze a nucleic acid sequence based on a set of sequence data, the computer program product comprising the following computer-readable program code for effecting actions in the computer:

• program code for identifying predetermined regions of the nucleic acid sequence based on the sequence data;
• program code for calculating a score for each identified region of the nucleic acid sequence, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓;
• program code for comparing the calculated score of each region to a predetermined threshold;
• and
• program code for identifying a probable coding region in the nucleic acid sequence based on the comparison of the score of each region to the predetermined threshold,
• wherein said program code for identifying predetermined regions comprises program code for locating each region of the nucleic acid sequence that is between splice sites.

A method for locating at least one exon within a nucleic acid sequence, said method comprising:

• identifying each region in the nucleic acid sequence that does not contain an internal stop codon;
• calculating a score of each region in the nucleic acid sequence;
• and
• determining the location of at least one exon in the nucleic acid sequence based on the score of each region of the sequence,
• wherein said identifying comprises identifying each stop-stop stretch (SSS) region in the nucleic acid sequence and said calculating comprises scoring the periodicity of each base in each SSS region at a frequency of ⅓ in accordance with a periodicity function.

A method for locating at least one exon within a nucleic acid sequence, said method comprising:

• identifying at least one region in the nucleic acid sequence with a jumping window;
• calculating a score of each region in the nucleic acid sequence;
• comparing the score of each identified region in the sequence to a predetermined
• threshold and flagging the region if the score of the region is greater than or equal to the
• predetermined threshold;
• expanding the borders of each flagged region until a maximum score for the flagged region is reached;
• identifying the longest, expanded flagged region;
• and
• determining the location of an exon in the sequence based on the longest, expanded flagged region that is identified,
• wherein said calculating comprises scoring the periodicity of each base in each jumping window region at a frequency of ⅓ in accordance with a periodicity function.

A method for determining whether a protein coding region of a nucleic acid sequence is full length, said method comprising:

• identifying a portion of the nucleic acid sequence that is upstream of the protein coding region of the sequence;
• calculating a score for the upstream portion of the nucleic acid sequence;
• and
• determining whether the protein coding region is full length based on the calculated score of the upstream portion of the nucleic acid sequence, said determining comprising comparing the score of the upstream portion of the sequence to a predetermined threshold, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓.

A method for determining whether a predetermined region of a nucleic acid sequence is full length, said method comprising:

• identifying a portion of the nucleic acid sequence that is upstream of the predetermined region of the sequence;
• combining the upstream portion of the sequence to the predetermined region of the sequence and calculating a score for the combined region;
• and
• determining whether the predetermined region is full length based on the calculated score of the combined region, wherein said calculating comprises examining the periodicity of each base in each region at a frequency of ⅓.