Patent ID: 9110872
Filing Date: 2015-08-18
Classification: G06F,G16B

Abstract:
1. A computer system-implemented method for storing and presenting sequence data, comprising: i) specifying a set of replets for analysis by a computer system; ii) for each replet in the set, comparing each replet by the computer system to a sequence for determining by the computer system a subsequence of the sequence that matches each replet, if any, wherein the sequence represents a genome sequence; iii) generating, by the computer system responsive to the comparing, respective entries of a match-set data structure, the match-set data structure having respective entries for the respective replets, each entry comprising a sequence identification to identify a sequence where a match occurs and offset information to determine a position within the sequence where the matching subsequence of the sequence is located, wherein the offset information comprises a first and second position parameter; iv) storing the generated entries of the match-set data structures in a computer readable memory by the computer system; v) deleting by the computer system each matching subsequence from the sequence where it is found; vi) concatenating by the computer system, in order, unmatched regions of sequences that remain after deleting each matching subsequence to form and store a backbone sequence; vii) the computer system generating or receiving a selection of at least a first one of the replets, wherein at least a portion of one of the matching subsequences is matched by a certain plurality of the replets and the received selection includes a selection of at least one of the certain plurality of replets; viii) the computer system generating a first instance of the sequence and presenting the first instance of the sequence to a user of the computer system, wherein the generating of the sequence is responsive to the stored backbone sequence and responsive to the at least one of the stored match-set data entries corresponding to the selected at least first one of the replets, wherein the first position parameter of each match-set data structure entry denotes a location in the sequence and the second position parameter of each match-set data structure entry denotes an offset from the location, wherein the selected at least first one of the replets has a position within the sequence, and wherein after receiving the selection the computer system updates the first and second parameters of the entries in the match-set data structure, the updating being responsive to the position of the selected at least first one of the replets; ix) the computer system generating or receiving a selection of a second one of the replets; and x) the computer system generating and presenting a second instance of the sequence to a user responsive to the at least second one of the replets and wherein the computer system performs the generating of the second instance of the sequence by reference to the updated first and second parameters for the second one of the replets.