Method of processing and/or genome mapping of diTag sequences
AssigneeAgency for Science, Technology and Research
InventorsKuo Ping Chiu, Yijun Ruan, Chia Lin Wei
Life of this patent
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Abstract
There is provided a method and system for processing and/or mapping ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment. The method of processing comprises preparing a database or file comprising at least one ditag sequence. The method of mapping comprises preparing a database or file of ditag(s), and mapping the ditag sequence(s) to the genome, comprising matching the 5′ and the 3′ terminal tags of the ditag sequence to at least a portion of the genome.
Claims18
A method of processing ditag nucleotide sequence(s) for mapping the ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment, the method comprising
- (i) preparing a database or file comprising at least one ditag sequence by extracting the ditag sequence(s) from sequences of at least one library comprising ditags, wherein each ditag sequence of the library of ditag(s) is flanked by a spacer nucleotide sequence and each ditag sequence is extracted from the library by inputting the spacer nucleotide sequence(s);
- (ii) matching the 5′ terminal tag to at least a portion of a genome sequence to identify at least one 5′ site having a sequence matching the 5′ terminal tag;
- (iii) matching the 3′ terminal tag to at least a portion of a genome sequence to identify at least one 3′ site having a sequence matching the 3′ terminal tag;
- (iv) identifying at least one occurring segment comprising a sequence segment along the genome sequence between one 5′ site and one 3′ site, each occurring segment having a sequence length;
- and
- (v) identifying at least one gene location comprising at least one occurring segment having a sequence length not exceeding that of a predefined gene length;
- wherein the extraction of ditag sequence(s), the genome mapping or both the extraction of ditag sequences and the genome mapping is/are carried out on a computer.
A computer for processing ditag nucleotide sequence(s), the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule, or fragment thereof or genome fragment, comprising at least one program, wherein the at least one program
- (i) prepares a database or file comprising at least one ditag sequence by extracting the ditag sequence(s) of at least one library comprising ditag(s), wherein each ditag sequence of the library of ditag(s) is flanked by a spacer nucleotide sequence and each ditag sequence is extracted from the library by inputting the spacer nucleotide sequence(s);
- (ii) matches the 5′ terminal tag to at least a portion of a genome sequence to identify at least a 5′ site having a sequence matching the 5′ terminal tag;
- (iii) matches the 3′ terminal tag to at least a portion of the genome sequence to identify at least a 3′ site having a sequence matching the 3′ terminal tag;
- (iv) identifies at least one occurring segment comprising a sequence segment along the genome sequence between one of the 5′ site and one of the 3′ site, each occurring segment having a sequence length;
- and
- (v) identifies at least one gene location comprising at least one occurring segment having a sequence length not exceeding that of a predefined gene length.
Dependencies are inferred from the claim text.