Methods for producing a paired tag from a nucleic acid sequence and methods of use thereof

US20060024681A1Inactive Publication Date: 2006-02-02APPL BIOSYSTEMS INC
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Patent Information

Authority / Receiving Office
US · United States
Current Assignee / Owner
APPL BIOSYSTEMS INC
Publication Date
2006-02-02
Estimated Expiration
Not applicable · inactive patent

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Abstract

Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5′ end tag and 3′ end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence. In a further embodiment, a method is provided for identifying nucleic acid sequences that encode at least two interacting proteins.
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Description

RELATED APPLICATION

[0001] This application claims the benefit of U.S. Provisional Application No. 60 / 516,080, filed Oct. 31, 2003.

[0002] The entire teachings of the above application are incorporated herein by reference.BACKGROUND OF THE INVENTION

[0003] Whole genome shotgun sequencing, assembly and finishing is typically the strategy of choice for microbial and fungal genome sequencing. The cost-advantages and simplicity of the whole genome approach relative to a BAC based or hybrid sequencing strategy argue strongly for its continued development and application in future sequencing projects. However, a major problem with the BAC-based approaches is the high cost and operational burden associated with the production of 15,000-25,000 individual BAC subclone libraries, the 15-20% waste associated with re-sequencing the vector, as well as the unavoidable E. coli contamination, the need to deal with transposon and bacteriophage insertions, and the 20-50% waste in redundant sequencing...

Claims

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