Genetic attribute analysis
A bioinformatics method, software, database and system for genetic attribute analysis are presented in which non-identical sets of genetic attributes comprising nucleotide sequences are compared to determine whether proteins encoded by those nucleotide sequences are functionally equivalent and, therefore, whether genetic information contained in the sets of genetic attributes can be considered equivalent. Sets of genetic attributes are determined to be equivalent based on whether they are able to satisfy one or more predetermined equivalence rules for comparing non-identical protein-encoding nucleotide sequences. A determination of equivalence between sets of genetic attributes can enable the compression of thousands of individual DNA nucleotide attributes into a single categorical attribute, as well as enable determinations of co-association of attributes, predisposition prediction and predisposition modification of individuals.
1 . A bioinformatics method for determining the equivalence of genetic attributes associated with individuals of a population, comprising:
a) accessing a first set of genetic attributes comprising a first nucleotide sequence containing an open reading frame encoding a protein associated with a first group of one or more individuals from the population;
b) accessing a second set of genetic attributes comprising a second nucleotide sequence containing an open reading frame encoding a protein associated with a second group of one or more individuals from the population, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;
c) identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on at least one equivalence rule for comparison of non-identical protein-encoding nucleotide sequences;
d) generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes and the second set of genetic attributes are equivalent; and
e) transmitting the determination as output.
2 . The bioinformatics method of claim 1 , wherein the output is transmitted to at least one destination selected from the group consisting of a user, a database, a dataset, a computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, and a wireless receiver.
3 . The bioinformatics method of claim 1 , further comprising:
f) generating, based on the determination, categorical attributes stored in association with attribute profiles of the first group of one or more individuals and the second group of one or more individuals to generate expanded attribute profiles.
4 . The bioinformatics method of claim 1 , further comprising:
f) computing, based on the determination, the frequencies of occurrence of the first set of genetic attributes and the second set of genetic attributes.
5 . The bioinformatics method of claim 1 , wherein the first group of one or more individuals is associated with a query attribute, and the second group of one or more individuals is not associated with the query attribute, the method further comprising:
f) computing, based on the determination, a statistical result indicating the strength of association of the first set of genetic attributes with the query attribute.
6 . The bioinformatics method of claim 1 , wherein the first set of genetic attributes is associated with a query attribute, the method further comprising:
f) generating, based on the determination, one or more statistical predictions indicating the predisposition of the second group of one or more individuals for association with the query attribute.
7 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more nucleotides within the open reading frame that do not alter the amino acid sequence of the protein.
8 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more nucleotides within the open reading frame that result in conservative amino acid substitutions within the amino acid sequence of the protein.
9 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more nucleotides within the open reading frame that result in conservative amino acid substitutions occurring anywhere within the protein except for enzymatic, transmembrane and antigen-recognition domains.
10 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more nucleotides within the open reading frame that result in silent amino acid substitutions within the protein.
11 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more conservative missense mutations within the open reading frame.
12 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more conservative missense mutations occurring anywhere within the open reading frame encoding the protein except for those regions of the open reading frame that encode enzymatic, transmembrane or antigen-recognition domains of the protein.
13 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by one or more silent mutations occurring within the open reading frame.
14 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by the locations of nonsense mutations within the open reading frame that occur within a same domain of the protein.
15 . The bioinformatics method of claim 1 , wherein the equivalence rule determines two protein-encoding nucleotide sequences to be equivalent if they encode the same protein and differ by the locations of frameshift mutations within the open reading frame that occur within a same domain of the encoded protein.
16 . A program storage device readable by a machine and containing a set of instructions which, when read by the machine, causes execution of a bioinformatics method for determining the equivalence of genetic attributes associated with individuals of a population, comprising:
a) accessing a first set of genetic attributes comprising a first nucleotide sequence containing an open reading frame encoding a protein associated with a first group of one or more individuals from the population;
b) accessing a second set of genetic attributes comprising a second nucleotide sequence containing an open reading frame encoding a protein associated with a second group of one or more individuals from the population, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;
c) identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on at least one equivalence rule for comparison of non-identical protein-encoding nucleotide sequences;
d) generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes and the second set of genetic attributes are equivalent; and
e) transmitting the determination as output.
17 . The program storage device of claim 16 , wherein the output is transmitted to at least one destination selected from the group consisting of a user, a database, a dataset, a computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, and a wireless receiver.
18 . A bioinformatics database system for determining the equivalence of genetic attributes associated with individuals of a population, comprising:
a) a memory containing:
i) a first data structure containing a first set of genetic attributes comprising a first nucleotide sequence containing an open reading frame encoding a protein associated with a first group of one or more individuals from the population;
ii) a second data structure containing a second set of genetic attributes comprising a second nucleotide sequence containing an open reading frame encoding a protein associated with a second group of one or more individuals from the population, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;
b) a processor for:
i) accessing the first data structure;
ii) accessing the second data structure;
iii) identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on at least one equivalence rule for comparison of non-identical protein-encoding nucleotide sequences;
iv) generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes and the second set of genetic attributes are equivalent; and
v) transmitting the determination as output.
19 . A bioinformatics computer-based system for determining the equivalence of genetic attributes associated with individuals of a population, comprising:
a) a first data accessing subsystem for accessing a first set of genetic attributes comprising a first nucleotide sequence containing an open reading frame encoding a protein associated with a first group of one or more individuals from the population;
b) a second data accessing subsystem for accessing a second set of genetic attributes comprising a second nucleotide sequence containing an open reading frame encoding a protein associated with a second group of one or more individuals from the population, wherein one or more nucleotides of the second nucleotide sequence differ from one or more nucleotides of the first nucleotide sequence;
c) a data processing subsystem comprising:
i) a data comparison subsystem for identifying whether the first nucleotide sequence and the second nucleotide sequence are equivalent based on at least one equivalence rule for comparison of non-identical protein-encoding nucleotide sequences;
ii) a data generating subsystem for generating, if the first nucleotide sequence and the second nucleotide sequence were identified to be equivalent, a determination indicating that the first set of genetic attributes and the second set of genetic attributes are equivalent; and
d) a communications subsystem for transmitting the determination as output.
20 . The bioinformatics computer-based system of claim 19 , wherein the output is transmitted to at least one destination selected from the group consisting of a user, a database, a dataset, a computer readable memory, a computer readable medium, a computer processor, a computer network, a printout device, a visual display, and a wireless receiver.