Computer-implemented processes of associating digital representations of each contiguous nucleic acid sequence polymorphism (CNSP) of particular sequence lengths between two (2) through and including ninety-nine (99) from the aggregate of the nucleic acid sequence data of both individuals that express an examined phenotype and individuals that do not express the phenotype, with the separate nucleic acid sequence data of each individual that expresses the phenotype and the separate nucleic acid sequence data of each individual that does not express the phenotype, comprised of the following steps:
- a) inputting nucleic acid sequence data which has been reduced to a single-letter nucleic acid digital form from an individual or individuals that express an examined phenotype and inputting other nucleic acid sequence data which has been reduced to a single-letter nucleic acid digital form from an individual or individuals that do not express the examined phenotype, into the data structures of a computer programming language and the permanent memory devices of a computer,
- b) reporting, if indicated by the computer user, separately for each sequence of each individual whose data is input, for display to a computer monitor and for output to a text file, the input nucleic acid sequence data or a subset of the input sequence data such as the first few dozen nucleic acids of the sequence,
- c) counting, if indicated by the computer user, separately for each sequence of each individual whose data is input, the number of nucleic acids of each type represented by the standard single-letter nomenclature A, C, T and G, summing the total for all four types in the aggregate, and reporting to a computer monitor and to a text file the separate counts of the number of each type of nucleic acid for each sequence and the sum of all four nucleic acids in the aggregate for the sequence,
- d) inputting an indication of whether input sequences are from individuals that express the examined phenotype or are from individuals that do not express the phenotype,
- e) inputting an indication of a particular sequence length between two and ninety-nine, or particular sequence lengths between two and ninety-nine, for the contiguous nucleotide sequence polymorphisms (CNSPs) that are associated with the sequence data of individuals that express the phenotype and the sequence data of individuals that do not express the phenotype,
- f) identifying and reporting to the computer monitor and text file, if indicated by the computer user, the number of contiguous nucleic acid sequences (CNSs) of each particular sequence length or lengths, including duplicates of the same sequence at the same length, separately for each input sequence from each individual whose sequence data was input, and also identifying and reporting, if indicated by the computer user, the aggregate number of all contiguous nucleic acid sequences (CNSs) at each particular sequence length or lengths, including duplicates of the same sequence at the same length, for the aggregate of all input sequences from all individuals whose sequence data was input,
- g) identifying and reporting to the computer monitor and text file, if indicated by the computer user, the number of contiguous nucleic acid sequence polymorphisms (CNSPs) of each particular sequence length or lengths, excluding duplicates of the same sequence at the same length, separately for each input sequence from each individual whose sequence data was input, and also identifying and reporting, if indicated by the computer user, the aggregate number of all contiguous nucleic acid sequence polymorphisms (CNSPs) at each particular sequence length, excluding duplicates of the same sequence at the same length, for the aggregate of all input sequences from all individuals whose sequence data was input,
- h) detecting whether each contiguous nucleic acid sequence polymorphism (CNSP) of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, occurs within the nucleic acid sequence data of each individual that expresses the phenotype and occurs within the nucleic acid sequence data of each individual that does not express the phenotype,
- i) counting for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, the number of individuals that express the phenotype on whose sequence data the CNSP occurs, and counting the number of individuals that express the phenotype on whose sequence data the CNSP does not occur, and counting the number of individuals that do not express the phenotype on whose sequence data the CNSP occurs, and counting the number of individuals that do not express the phenotype on whose sequence data the CNSP does not occur,
- j) computing for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, based on the foregoing counts of occurrence, the percentage of individuals that express the phenotype on whose sequence data the CNSP occurs and the percentage of individuals that do not express the phenotype on whose sequence data the CNSP occurs,
- k) computing for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, based on the foregoing counts of occurrence, the relative risk ratio of the percentage of individuals that express the phenotype on whose sequence data the CNSP occurs to the percentage of individuals that do not express the phenotype on whose sequence data the CNSP occurs,
- l) computing for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, based on the foregoing counts of occurrence, the chi square statistic as to the likelihood that the difference in the number of individuals that express the phenotype on whose sequence data the CNSP occurs and does not occur relative to the number of individuals that do not express the phenotype on whose sequence data the CNSP occurs and does not occur can be attributed to random sampling fluctuations as opposed to non-chance factors,
- m) computing for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, based on the foregoing counts of occurrence, phi correlation coefficients of the strength of the relationship between the occurrence of the CNSP on the sequence data of examined individuals and the expression of the phenotype in these individuals,
- n) selecting for reporting from each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, the range of the number of individuals that express the phenotype on whose sequence data the CNSP occurs, the range of the number of individuals that express the phenotype on whose sequence data the CNSP does not occur, the range of the number of individuals that do not express the phenotype on whose sequence data the CNSP occurs, and the range of the number of individuals that do not express the phenotype on whose sequence data the CNSP does not occur,
- o) selecting for reporting from each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, the range of the percentage of individuals that express the phenotype on whose sequence data the CNSP occurs, and the range of the percentage of individuals that do not express the phenotype on whose sequence data the CNSP occurs,
- p) selecting for reporting from each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, the range of the the computed relative risk, chi square, and phi correlation coefficient measures of association,
- q) reporting, if indicated by the computer user, for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, for the sequence data of each individual that expresses the phenotype and the sequence data of each individual that does not express the phenotype, the values of the relative risk, chi square, and phi correlation coefficient measures of association if within the selected ranges, and for those values not within the selected ranges the empty set, listed by CNSP with value or empty set in the order that the CNSP occurs on the nucleic acid sequence data of individuals,
- r) reporting, for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, the selected range of the numbers of occurrence and the selected range of the percentages of occurrence, and reporting the selected range of the relative risk values, chi square values, and phi correlation coefficient values, listed alphabetically by CNSP with value and listed by values with CNSP,
- s) reporting for each CNSP of a particular sequence length or lengths from the aggregate of the nucleic acid sequence data of both individuals that express the phenotype and individuals that do not express the phenotype, for the selected the range of the percentage of individuals that express the phenotype on whose sequence data the CNSP occurs and the range of the percentage of individuals that do not express the phenotype on whose sequence data the CNSP occurs, each originating and each and derivative CNSP, and a summary of the number of CNSPs that meet the percentages for each sequence length from two through ten.