Systems, methods, and devices for analysis of genetic material

A computer-implemented method, implemented by hardware in combination with software, said method comprising:

• (A) for each particular nucleic acid sequence of a plurality of nucleic acid sequences, wherein said plurality of nucleic acid sequences correspond to a plurality of transcripts of a particular human gene, said particular human gene having multiple transcripts, and
• wherein said particular nucleic acid sequence represents at least part of a particular transcript of said particular human gene, and wherein said particular transcript of said particular human gene comprises multiple introns, and wherein said particular nucleic acid sequence has a length n,
• and wherein at least one transcript of said particular human gene corresponds to a particular protein, and wherein at least some of said particular nucleic acid corresponds to a plurality of said multiple introns:
• (A)(0) determining a plurality k of subsequences of a representation of said nucleic acid sequence, wherein the number of subsequences k is a function of n2;
• (A)(1) determining a plurality of subsequence portion signature values corresponding to said plurality of subsequences, wherein, for a given subsequence of said plurality of subsequences, the corresponding subsequence portion signature value is based on a first computational function applied to a representation of said given subsequence;
• (A)(2) determining an intron portion signature value from said subsequence portion signature values, said intron portion signature value being determined based on a computational function applied to said plurality of subsequence portion signature values, said intron portion signature value comprising a unique sequence identifier for said nucleic acid sequence;
• (A)(3) determining a particular protein signature value corresponding to said particular protein;
• (A)(4) forming, in a database, an association between one or more of said intron portion signature values and said particular protein signature value, wherein each of said intron portion signature values is associated with a corresponding unique sequence identifier in the database;
• and then
• (B) applying a sort to fields in said database, said sort being keyed on unique sequence identifiers associated with intron portion signature values in the database, and then
• (C) determining an order for a plurality of nucleic acid sequences in said database based on said sort;
• and then
• (D) using said order to evaluate and/or determine a role and/or function of a portion of at least one transcript of said particular human gene and a given protein.

A computer-implemented method, implemented by hardware in combination with software, said method comprising:

• (a) determining an order of a given intron portion signature value associated with a given nucleic acid sequence from a given transcript of a particular human gene relative to intron portion signature values associated with nucleic acid sequences of multiple other transcripts of said particular human gene, wherein said given transcript of said particular human gene comprises multiple introns, and wherein said given nucleic acid sequence corresponds to a plurality of said multiple introns, said order being based on unique sequence identifiers associated with intron portion signature values in a database;
• (b) applying a sort to fields in the database, said sort keyed on unique sequence identifiers associated with intron portion signature values in the database;
• and
• (c) using said order to evaluate and/or determine a role and/or function of at least one transcript of said particular human gene or said given nucleic acid sequence and a given protein,
• wherein said database comprises multiple associations, each association being between one or more intron portion signature values and corresponding protein signature values, wherein a particular protein signature value corresponds to a particular protein,
• each of said intron portion signature values corresponding to multiple introns of a corresponding transcript of said particular human gene, each of said intron portion signature values being based on a first computational function applied to a plurality k of subsequence portion signature values corresponding to intron portions of a particular nucleic acid sequence corresponding to said multiple introns, wherein, for a particular nucleic acid sequence of length n, the number k of subsequence portion signature values is O(n2), and
• wherein, in said database, each of said intron portion signature values is associated with a corresponding unique sequence identifier, and
• wherein said particular nucleic acid sequence represents at least a portion of a particular human gene, and wherein at least one transcript of said particular human gene corresponds to a particular protein, and wherein said particular nucleic acid sequence corresponds to at least a portion of at least one intron of said particular human gene.