Claims
- 1. A method for identifying evolutionarily conserved or divergent sequences, comprising the steps of:
collecting a plurality of hybridization intensities wherein each of said intensities reflects the hybridization of one of a plurality of probes from a first nucleic acid sequence from a first organism to a sample nucleic acid from a second organism, wherein said probes are complementary and non-complementary to a known nucleic acid sequence from said first organism, wherein said probes are arrayed on a substrate and wherein each detection probe is at a known location on said substrate; identifying bases of said plurality of probes according to said hybridization intensities; and calculating an identity index between said first nucleic acid sequence from said first organism and said sample nucleic acid from said second organism.
- 2. The method of claim 1, wherein said detection probes are sets of four probes where one probe of said probe set is perfectly complementary to said known nucleic acid sequence and three probes of said probe set are non-complementary to said known nucleic acid sequence.
- 3. The method of claim 2, wherein said non-complementary probes differ from said known nucleic acid sequence by one base.
- 4. The method of claim 3, wherein said one base is a base located at or near a central position of said probe.
- 5. The method of claim 1, wherein said sample nucleic acids are nucleic acids which have been amplified by the polymerase chain reaction.
- 6. The method of claim 1, wherein said identity index is calculated by determining a percentage of similarity between sub-regions of said nucleic acids from said first organism and said nucleic acids from said second organism
- 7. The method of claim 6, wherein said sub-regions are overlapping, moving windows of base pairs across said nucleic acid sequence from a first organism.
- 8. The method of claim 7, wherein said windows are between about 20 base pairs and 150 base pairs.
- 9. The method of claim 7, wherein said overlap of said windows is between about 5 base pairs and about 75 base pairs.
- 10. A method for screening for functional sequences in a genome of a first organism, comprising the steps of:
providing a substrate having a plurality of detection probes, wherein each detection probe is at a known location, and wherein at least one of said detection probes is complementary to a known nucleic acid sequence in the genome from said first organism and at least one of said detection probes is non-complementary to a known nucleic acid sequence in the genome from said first organism; contacting at least one sample nucleic acid from a second organism with said substrate, where said second organism diverged evolutionarily from said first organism between about 60 million years ago and about 120 million years ago, and where said contacting is performed under conditions wherein when said at least one sample nucleic acid is substantially complementary to a detection probe said at least one sample nucleic acid will preferentially hybridize to a detection probe to which it is most complementary, resulting in at least one hybridized detection probe; determining a location of said at least one hybridized detection probe; and identifying sequences of said at least one hybridized detection probe by referring to the location of said at least one hybridized detection probe; wherein when said sequence of said at least one hybridized detection probe is the same as a sequence complementary to said known nucleic acid sequence from said first organism, there is sequence similarity between nucleic acids from said first organism and said second organism, and regions in said nucleic acids of said first organism where there is sequence similarity with said nucleic acids from said second organism are candidate functional regions in said nucleic acids of said first organism.
- 11. The method of claim 10, wherein said detection probes are sets of four probes where one probe of said probe set is perfectly complementary to said known nucleic acid sequence and three probes of said probe set are non-complementary to said known nucleic acid sequence.
- 12. The method of claim 11, wherein said non-complementary probes differ from said known nucleic acid sequence by one base.
- 13. The method of claim 12, wherein said one base is a base located at or near a central position of said probe.
- 14. The method of claim 10, wherein said probes are at least 18 bases long.
- 15. The method of claim 10, wherein said sample nucleic acids are nucleic acids which have been amplified by the polymerase chain reaction.
- 16. The method of claim 10, further comprising the step of calculating an identity index between sub-regions of said nucleic acids from said first organism and said nucleic acids from said second organism.
- 17. The method of claim 16, wherein said identity index is calculated by determining a percentage of similarity between sub-regions of said nucleic acids from said first organism and said nucleic acids from said second organism.
- 18. The method of claim 17, wherein said sub-regions are overlapping, moving windows of base pairs across said nucleic acid sequence from a first organism.
- 19. The method of claim 18, wherein said windows are between about 20 base pairs and 150 base pairs.
- 20. The method of claim 18, wherein said overlap of said windows is between about 5 base pairs and about 75 base pairs.
RELATED APPLICATIONS
[0001] This application claims priority to provisional application U.S. Ser. No. 60/284,436 filed Apr. 18, 2001, which is incorporated by reference in its entirety for all purposes.
Provisional Applications (1)
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Number |
Date |
Country |
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60284436 |
Apr 2001 |
US |