Computer method and system for correlating data

A method in a computer system for simultaneously determining the sequence of a plurality of sample oligonucleotides (ODNs), each sequence having four bases A, T, C, and G, the method comprising:

• for each of the plurality of sample ODNs, receiving an indication of four molecular weights of molecular tags associated with the sample ODN, each of the four molecular weights corresponding to one of the four bases, each molecular weight being unique among all the molecular weights of all the molecular tags to be applied to all sample ODNs;
• and
• for each of a plurality of positions corresponding to a sequence length,
• receiving an indication of the molecular weights of the molecular tags that have been associated with synthesized ODNs comprising base sequences identical to portions of the sample ODNs, the tags separated based on a characteristic of the associated synthesized ODNs other than the sequence of the associated synthesized ODNs and subsequently dissociated from the synthesized ODNs, the molecular weights being detected by a mass spectrometer, wherein the mass spectrometer detects one of the four molecular weights assigned to each of the plurality of sample ODNs for each position;
• and
• for each of the plurality of sample ODNs,
• determining the base to which the detected molecular weight is assigned using the received indications for the sample ODN;
• and
• setting the base at the position in the sequence for the sample ODN.

A method in a computer system for determining whether a plurality of pairs of a test fragment and a reference fragment of DNA are different, the method comprising:

• for each of the plurality of pairs of fragments, at various times, receiving an indication of the number of a molecular tag with a unique molecular weight that is associated with, but subsequently dissociated from, the pair of fragments, wherein the tags are separated based on a characteristic of the associated DNA fragments other than the sequences of the DNA fragments before the dissociation of the tag from the DNA fragments;
• and
• for each of the unique molecular weights of the molecular tags,
• determining whether there is more than one peak in the number of molecular tags detected for that molecular weight;
• and
• indicating that the pair of DNA fragments are different when it is determined that there is more than one peak in the number of molecular tags detected for that molecular weight.

A method in a computer system for identifying whether two populations of mRNA are different, the method comprising:

• for each of a plurality of primers, at various times, receiving an indication of the number of a molecular tag with a unique molecular weight, the molecular tag being associated with the cDNA derived from the mRNA using each of the primers, separated based on a characteristic of the cDNA other than the sequence of the cDNA, and subsequently dissociated from the cDNA;
• and
• for each of the unique molecular weights of molecular tags,
• comparing the presence of a peak in the number of molecular tags detected for that molecular weight at any particular time derived from one population of mRNA with that of the other population;
• and
• indicating that the two populations of mRNA are different when there is a difference in the presence of the peak.

A computer system for correlating known characteristics of nucleic acid molecules to molecular tags with unique molecular weights that have been associated with the nucleic acid molecules or portions thereof, comprising:

• a molecular tag definition table indicating the molecular weight of each molecular tag;
• a defined run component for generating a mapping of each nucleic acid molecule to a molecular tag;
• a molecular weight collection component for receiving an indication of the molecular weights of the molecular tags that have been associated with the nucleic acid molecules or portions thereof, separated based on a determined characteristic of the associated nucleic acid molecules or portions thereof other than the sequences of the nucleic acid molecules, and subsequently dissociated from the nucleic acid molecules or portions thereof;
• and
• a correlation component that determines, based on the received mapping, the known characteristic of the nucleic acid molecule corresponding to the detected molecular weight, and indicates that the nucleic acid molecule has the determined characteristic.