Efficient methods and apparatus for high-throughput processing of gene sequence data

A computer program product comprising:

• a computer-usable storage medium;
• computer-readable program code embodied on said computer-usable storage medium;
• and
• the computer-readable program code for effecting the following acts on a computer:
• reading gene sequence data corresponding to a gene sequence and coding sequence data corresponding to a plurality of coding sequences within the gene sequence;
• identifying primer pair data within the gene sequence data by following a set of primer selection rules, the primer pair data corresponding to a pair of primer sequences for one of the coding sequences, the set of primer selection rules including a first rule specifying that the primer pair data be obtained for a predetermined annealing temperature;
• storing the primer pair data;
• repeating the acts of identifying and storing such that primer pair data are obtained for each sequence of the plurality of coding sequences at the predetermined annealing temperature, so that the plurality of coding sequences can be simultaneously amplified in gene sequences from three or more of individuals at the predetermined annealing temperature using the identified pairs of primer sequences to produce a plurality of amplified coding sequences from the three or more individuals.

A method of processing gene sequence data with use of one or more computers, the method comprising:

• reading, by the computer, a plurality of nucleotide base identifier strings;
• positionally aligning, by the computer, the plurality of nucleotide base identifier strings to produce a plurality of aligned nucleotide base identifier strings;
• performing, by the computer, a comparison amongst aligned nucleotide base identifiers at each nucleotide base position of the plurality of aligned nucleotide base identifier strings;
• performing, by the computer, a comparison amongst aligned nucleotide base identifiers at each nucleotide base position of the plurality of aligned nucleotide base identifier strings;
• at each nucleotide base position where a difference amongst aligned nucleotide base identifiers exists:
• reading, by the computer, nucleotide base quality information associated with the aligned nucleotide base identifiers where the difference exists;
• comparing, by the computer, the nucleotide base quality information with predetermined qualification data;
• visually displaying, from the computer, the nucleotide base quality information for acceptance or rejection;
• and
• if the nucleotide base quality information meets the predetermined qualification data and is accepted:
• providing and storing resulting data that identifies where the difference amongst the aligned base identifiers exists.

A computer program product comprising:

• a computer-usable storage medium;
• computer-readable program code embodied on said computer-usable storage medium;
• and
• the computer-readable program code for effecting the following acts on a computer:
• reading a plurality of nucleotide base identifier strings;
• positionally aligning the plurality of nucleotide base identifier strings to produce a plurality of aligned nucleotide base identifier strings;
• performing a comparison amongst aligned nucleotide base identifiers at each nucleotide base position of the plurality of aligned nucleotide base identifier strings;
• performing a comparison amongst aligned nucleotide base identifiers at each nucleotide base position of the plurality of aligned nucleotide base identifier strings;
• at each nucleotide base position where a difference amongst aligned nucleotide base identifiers exists:
• reading nucleotide base quality information associated with the aligned nucleotide base identifiers where the difference exists;
• comparing the nucleotide base quality information with predetermined qualification data;
• visually displaying the nucleotide base quality information for acceptance or rejection;
• and
• if the nucleotide base quality information meets the predetermined qualification data and is accepted:
• providing and storing resulting data that identifies where the difference amongst the aligned base identifiers exists.

A method of processing gene sequence data with use of one or more computers, the method comprising:

• reading, by the computer, gene sequence data corresponding to a gene sequence and coding sequence data corresponding to a plurality of coding sequences within the gene sequence;
• identifying, by the computer following a set of primer selection rules, primer pair data within the gene sequence data, the primer pair data corresponding to a pair of primer sequences for one of the coding sequences, the set of primer selection rules including a first rule specifying that the primer pair data be obtained for a predetermined annealing temperature and a second rule specifying that a single primer pair be identified for two or more coding regions if they are sufficiently close together;
• storing, by the computer, the primer pair data;
• and
• repeating the acts of identifying and storing such that primer pair data are obtained for the plurality of coding sequences at the predetermined annealing temperature.