Transcript mapping method

• US 20060057586A1
• Filed: 09/13/2004
• Published: 03/16/2006
• Est. Priority Date: 09/13/2004
• Status: Active Grant

• Current Assignee: Agency For Science Technology and Research
• Original Assignee: Agency For Science Technology and Research
• Inventors: Ruan, Yijun, Sung, Wing Kin Ken
• Granted Patent: US 8,005,621 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, the 5′ and 3′ ends of full-length cDNA clones are initially extracted into a ditag structure, with the ditag concatemers of the ditag being subsequently sequenced in an efficient manner, and finally mapped to the genome for defining the gene structure. As a GIS ditag represents the 5′ and 3′ ends of a transcript, it is more informative than SAGE and MPSS tags. Segment lengths between 5′ and 3′ tag pairs are obtainable including orientation, ordering and chromosome family for efficient transcript mapping and gene location identification. Furthermore, a compressed suffix array (CSA) is used for indexing the genome sequence for improve mapping speed and to reduce computational memory requirements.

Claims

1. A transcript mapping method comprising the steps of:

obtaining a 5′

terminal tag and a 3′

terminal tag from a transcript of a gene;

matching the 5′

terminal tag to at least a portion of a genome sequence to thereby identify at least one 5′

site therefrom, each of the at least one 5′

site having a sequence matching the 5′

terminal tag;

matching the 3′

terminal tag to at least a portion of the genome sequence to thereby identify at least one 3′

site therefrom, each of the at least one 5′

site having a sequence matching the 5′

terminal tag;

identifying at least one occurring segment, each of the at least one occurring segment being a sequence segment along the genome sequence extending from one of the at least one 5′

site to one of the at least one 3′

site, each of the at least one occurring segment having a sequence length; and

identifying at least one feasible gene location, each of the feasible gene location being one of the at least one occurring segment having a sequence length not exceeding that of a predefined gene length.

2. The transcript mapping method as in claim 1, the step of identifying a 5′

terminal tag and a 3′

terminal tag comprising the step of;

providing a nucleotide sequence with at least 16 base pairs for forming the 5′

terminal tag; and

providing a nucleotide sequence with at least 16 base pairs for forming the 3′

terminal tag.

3. The transcript mapping method as in claim 1, the step of matching the 5′

terminal tag to at least a portion of a genome sequence comprising the step of;

matching the 5′

terminal tag to a chrosmosome sequence.

4. The transcript mapping method as in claim 3, the step of matching the 3′

terminal tag to at least a portion of the genome sequence comprising the step of;

matching the 3′

terminal tag to a chrosmosome sequence.

5. The transcript mapping method as in claim 1, further comprising the step of generating a data structure for indexing the genome sequence.

6. The transcript mapping method as in claims 1, further comprising the step of generating at least one of a tree structure and an ordered array for indexing the genome sequence.

7. The transcript mapping method as in claims 1, further comprising the step of generating at least one of a suffix array, a suffix tree, a binary tree and a compressed suffix array for indexing the genome sequence.

8. The transcript mapping method as in claim 7, the step of the matching the 5′

terminal tag to at least a portion of a genome sequence comprising the step of;

at least one of forward traversing and reverse traversing the genome sequence for comparing the 5′

terminal tag to at least a portion of the genome sequence to obtain the at least one 5′

site.

9. The transcript mapping method as in claim 8, the step of the matching the 3′

terminal tag to at least a portion of a genome sequence comprising the step of;

at least one of forward traversing and reverse traversing the genome sequence for comparing the 3′

terminal tag to at least a portion of the genome sequence to obtain the at least one 3′

site.

10. The transcript mapping method as in claim 1, the step of identifying at least one feasible gene location comprising the step of comparing sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto to at least a portion of the genome sequence for obtaining the at least one feasible gene location therefrom.

11. The transcript mapping method as in claim 10, the step of comparing sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto comprising the step of comparing the sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto being in accordance with a 5′

-occurring segment-3′

structure.

12. The transcript mapping method as in claim 1, the step of identifying at least one feasible gene location comprising the step of identifying the 5′

-3′

orientation of each of the at least one occurring segment for obtaining the at least one feasible gene location therefrom.

13. The transcript mapping method as in claim 12, the step of identifying the 5′

-3′

orientation comprising the step of identifying a residual AA neucleotide, the residual AA neucleotide constituting a portion of the 3′

terminal tag.

14. The transcript mapping method as in claim 1, the step of identifying at least one feasible gene location comprising the step of:

identifying the chromosome wherein each of one of the at least one 5′

site and one of the at least one 3′

site corresponding to each of the occurring segment is located for identifying the at least one feasible gene location therefrom.

15. The transcript mapping method as in claim 1, the step of matching the 5′

terminal tag to at least a portion of a genome sequence comprising the step of;

identifying quantity of the at least one 5′

site, and the step of matching the 3′

terminal tag to at least a portion of a genome sequence comprising the step of;

identifying quantity of the at least one 3′

site.

16. The transcript mapping method as in claim 15, the step of identifying at least one occurring segment comprising the step of:

traversing along the genome sequence towards one of the extremities thereof from each of the at least one 5′

site for identifying at least one of the at least one 3′

site.

17. The transcript mapping method as in claim 16, the step of identifying the at least one feasible gene location comprising the step of:

terminating traversal along the genome sequence in response to one of the at least one feasible gene location being identified for each of the at least one 5′

site.

18. The transcript mapping method as in claim 15, the step of identifying at least one occurring segment comprising the step of:

traversing along the genome sequence towards one of the extremities thereof from each of the at least one 3′

site for identifying at least one of the at least one 5′

site.

19. The transcript mapping method as in claim 18, the step of identifying the at least one feasible gene location comprising the step of:

terminating traversal along the genome sequence in response to one of the at least one feasible gene location being identified for each of the at least one 3′

site.

20. A transcript mapping system comprising:

means for obtaining a 5′

terminal tag and a 3′

terminal tag from a transcript of a gene;

means for matching the 5′

terminal tag to at least a portion of a genome sequence to thereby identify at least one 5′

site therefrom, each of the at least one 5′

site having a sequence matching the 5′

terminal tag;

means for matching the 3′

terminal tag to at least a portion of the genome sequence to thereby identify at least one 3′

site therefrom, each of the at least one 3′

site having a sequence matching the 3′

terminal tag;

means for identifying at least one occurring segment, each of the at least one occurring segment being a sequence segment along the genome sequence extending from one of the at least one 5′

site to one of the at least one 3′

site, each of the at least one occurring segment having a sequence length; and

means for identifying at least one feasible gene location, each of the feasible gene location being one of the at least one occurring segment having a sequence length not exceeding that of a predefined gene length.

21. The transcript mapping system as in claim 20, the means for identifying a 5′

terminal tag and a 3′

terminal tag comprising;

means for providing a nucleotide sequence with at least 16 base pairs for forming the 5′

terminal tag; and

means for providing a nucleotide sequence with at least 16 base pairs for forming the 3′

terminal tag.

22. The transcript mapping system as in claim 20, the means for matching the 5′

terminal tag to at least a portion of a genome sequence comprising;

means for matching the 5′

terminal tag to a chrosmosome sequence.

23. The transcript mapping system as in claim 22, the means for matching the 3′

terminal tag to at least a portion of the genome sequence comprising;

means for matching the 3′

terminal tag to a chrosmosome sequence.

24. The transcript mapping system as in claim 20, further comprising:

means for generating a data structure for indexing the genome sequence.

25. The transcript mapping system as in claims 20, further comprising:

means for generating at least one of a tree structure and an ordered array for indexing the genome sequence.

26. The transcript mapping system as in claims 20, further comprising:

means for generating at least one of a suffix array, a suffix tree, a binary tree and a compressed suffix array for indexing the genome sequence.

27. The transcript mapping system as in claim 26, the means for matching the 5′

terminal tag to at least a portion of a genome sequence comprising;

means for at least one of forward traversing and reverse traversing the genome sequence for comparing the 5′

terminal tag to at least a portion of the genome sequence to obtain the at least one 5′

site.

28. The transcript mapping system as in claim 27, the means for matching the 3′

terminal tag to at least a portion of a genome sequence comprising;

means for at least one of forward traversing and reverse traversing the genome sequence for comparing the 3′

terminal tag to at least a portion of the genome sequence to obtain the at least one 3′

site.

29. The transcript mapping system as in claim 20, the means for identifying at least one feasible gene location comprising:

means for comparing sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto to at least a portion of the genome sequence for obtaining the at least one feasible gene location therefrom.

30. The transcript mapping system as in claim 29, the means for comparing sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto comprising the means for comparing the sequence order of each of the at least one occurring segment and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto being in accordance with a 5′

-occurring segment-3′

structure.

31. The transcript mapping system as in claim 20, the means for identifying at least one feasible gene location comprising:

means for identifying the 5′

-3′

orientation of each of the at least one occurring segment for obtaining the at least one feasible gene location therefrom.

32. The transcript mapping system as in claim 31, the means for identifying the 5′

-3′

orientation comprising;

means for identifying a residual AA neucleotide, the residual AA neucleotide constituting a portion of the 3′

terminal tag.

33. The transcript mapping system as in claim 20, the means for identifying at least one feasible gene location comprising:

means for identifying the chromosome wherein each of one of the at least one 5′

site and one of the at least one 3′

site corresponding to each of the occurring segment is located for identifying the at least one feasible gene location therefrom.

34. The transcript mapping system as in claim 20, the means for matching the 5′

terminal tag to at least a portion of a genome sequence comprising;

means for identifying quantity of the at least one 5′

site, and the means for matching the 3′

terminal tag to at least a portion of a genome sequence comprising;

means for identifying quantity of the at least one 3′

site.

35. The transcript mapping system as in claim 34, the means for identifying at least one occurring segment comprising:

means for traversing along the genome sequence towards one of the extremities thereof from each of the at least one 5′

site for identifying at least one of the at least one 3′

site.

36. The transcript mapping system as in claim 35, the means for identifying the at least one feasible gene location comprising:

means for terminating traversal along the genome sequence in response to one of the at least one feasible gene location being identified for each of the at least one 5′

site.

37. The transcript mapping system as in claim 34, the means for identifying at least one occurring segment comprising:

means for traversing along the genome sequence towards one of the extremities thereof from each of the at least one 3′

site for identifying at least one of the at least one 5′

site.

38. The transcript mapping system as in claim 37, the means for identifying the at least one feasible gene location comprising:

means for terminating traversal along the genome sequence in response to one of the at least one feasible gene location being identified for each of the at least one 3′

site.

39. A transcript mapping method comprising the steps of:

obtaining a 5′

terminal tag and a 3′

terminal tag from a transcript of a gene;

matching the 5′

terminal tag to at least a portion of a genome sequence to thereby identify at least one 5′

site therefrom, each of the at least one 5′

site having a sequence matching the 5′

terminal tag;

matching the 3′

terminal tag to at least a portion of the genome sequence to thereby identify at least one 3′

site therefrom, each of the at least one 5′

site having a sequence matching the 5′

terminal tag;

identifying at least one occurring segment, each of the at least one occurring segment being a sequence segment along the genome sequence extending from one of the at least one 5′

site to one of the at least one 3′

site, each of the at least one occurring segment having a sequence length; and

identifying at least one feasible gene location from the at least one occurring segment, each of the at least one feasible gene location being one of the at least one occurring segment with at least one of the sequence length thereof not exceeding that of the predefined gene length, the sequence order thereof and of the at least one 5′

site and one of the at least one 3′

site corresponding thereto in accordance with a 5′

-occurring segment-3′

structure matching the sequence order of the corresponding portion of the genome sequence, the 5′

site and one of the at least one 5′

site and one of the at least one 3′

site corresponding thereto having a 5′

-3′

orientation, and one of the at least one 5′

site and one of the at least one 3′

site corresponding to each of the occurring segment being located within the same chromosome.