A computer implemented method for estimating a possibility of splicing having occurred in a gene region of interest, the method comprising: a) creating a read sequence database by sorting all read sequences of a cDNA obtained by a massively parallel DNA sequencer, as well as cyclic permutations or suffixes thereof in lexicographic order, wherein the read sequences are input by a user, b) creating a genome sequence database by inspecting a length of bases at which a partial sequence starting from each base position of a plurality of reference genome sequences, which are provided by a user, becomes unique in the reference genome sequence, and taking a complementary strand into consideration, and storing such information, so as to be able to quickly return a "Minimal Length of Uniqueness", MLU, c) obtaining a MLU, having a value "(L(x))" for each "X" in a range of "Xmin" to "Xmax", input by auser, at which a partial sequence starting from a position "X", in the reference genome sequence data becomes unique, by inquiring of the genome sequence database, d) obtaining a depth "D(x))" at each "X" by inquiring of the read sequence database, the depth being a number of the read sequences that contain the partial sequence as a key sequence, e) estimating the presence or absence of splicing at "X" by setting "X" to "Xmin" at a left end of a region of interest defined by parameters "Xmin" and "Xmax" input by a user, f) updating the value of "X" to "x + 1" if there is no splicing or estimation cannot be performed, and, otherwise, to select another base position g) determining a splicing event to have occurred at position "X", if the depth D(x) at position "X" is significantly smaller in a neighboring region of "X" on a backward direction side, which is genome coordinate decreasing direction, than in a neighboring region of "X" on a forward direction side, h) outputting position "X" as a position at which splicing may have occurred. a) creating a read sequence database by sorting all read sequences of a cDNA obtained by a massively parallel DNA sequencer, as well as cyclic permutations or suffixes thereof in lexicographic order, wherein the read sequences are input by a user, b) creating a genome sequence database by inspecting a length of bases at which a partial sequence starting from each base position of a plurality of reference genome sequences, which are provided by a user, becomes unique in the reference genome sequence, and taking a complementary strand into consideration, and storing such information, so as to be able to quickly return a "Minimal Length of Uniqueness", MLU, c) obtaining a MLU, having a value "(L(x))" for each "X" in a range of "Xmin" to "Xmax", input by auser, at which a partial sequence starting from a position "X", in the reference genome sequence data becomes unique, by inquiring of the genome sequence database, d) obtaining a depth "D(x))" at each "X" by inquiring of the read sequence database, the depth being a number of the read sequences that contain the partial sequence as a key sequence, e) estimating the presence or absence of splicing at "X" by setting "X" to "Xmin" at a left end of a region of interest defined by parameters "Xmin" and "Xmax" input by a user, f) updating the value of "X" to "x + 1" if there is no splicing or estimation cannot be performed, and, otherwise, to select another base position g) determining a splicing event to have occurred at position "X", if the depth D(x) at position "X" is significantly smaller in a neighboring region of "X" on a backward direction side, which is genome coordinate decreasing direction, than in a neighboring region of "X" on a forward direction side, h) outputting position "X" as a position at which splicing may have occurred.