TAGGED-FRAGMENT MAP ASSEMBLY
First Claim
1. A method for determining a sequence of a biomolecule, the method comprising the steps of:
- a) creating a biomolecule fragment from the biomolecule;
b) binding a plurality of uniform probes to the biomolecule fragment;
c) identifying a plurality of binding sites along the biomolecule fragment at which the probes bind to the biomolecule;
d) creating a collection of binding signatures for the biomolecule fragment, each binding signature representing a series of distances between binding sites within the fragment;
e) grouping the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature;
f) for each binding signature in a first cluster, selecting a potential successor binding signature from signature clusters other than the first signature cluster;
g) identifying one of the potential successor binding signatures as a successor binding signature;
h) repeating steps f) and g) until the successor signature represents a terminal signature, resulting in a sequence of signatures representing at least a portion of the biomolecule.
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Accused Products
Abstract
A method for determining a sequence of a biomolecule, the method including binding a plurality of uniform probes to a biomolecule fragment, creating a collection of binding signatures for the fragment with each binding signature representing a series of distances between binding sites within the fragment, and grouping the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature. For each binding signature in a first cluster, a potential successor binding signature is selected from signature clusters other than the first signature cluster, and one of the potential successor binding signatures is identified as a successor binding signature. The last two steps are repeated until the successor signature represents a terminal signature, resulting in a sequence of signatures representing at least a portion of the biomolecule.
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Citations
14 Claims
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1. A method for determining a sequence of a biomolecule, the method comprising the steps of:
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a) creating a biomolecule fragment from the biomolecule; b) binding a plurality of uniform probes to the biomolecule fragment; c) identifying a plurality of binding sites along the biomolecule fragment at which the probes bind to the biomolecule; d) creating a collection of binding signatures for the biomolecule fragment, each binding signature representing a series of distances between binding sites within the fragment; e) grouping the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature; f) for each binding signature in a first cluster, selecting a potential successor binding signature from signature clusters other than the first signature cluster; g) identifying one of the potential successor binding signatures as a successor binding signature; h) repeating steps f) and g) until the successor signature represents a terminal signature, resulting in a sequence of signatures representing at least a portion of the biomolecule. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A system for determining a sequence of a biomolecule, the system comprising:
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a) an identifying module that identifies a plurality of binding sites along a fragment of the biomolecule at which a plurality of uniform probes are bound; b) a signature-creating module that creates a collection of binding signatures for the fragment, each binding signature representing a series of distances between binding sites within the fragment; c) a grouping module that groups the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature; d) a selecting module that selects, for each binding signature in a first cluster, a potential successor binding signature from signature clusters other than the first signature cluster; and e) a sequencing module that (i) identifies one of the potential successor binding signatures as a successor binding signature, and (ii) determines the sequence of at least a portion of the biomolecule based at least in part on a series of identified successor binding signatures.
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13. An article of manufacture having computer-readable program portions embodied thereon for sequencing a biomolecule, the article comprising computer-readable instructions for:
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a) creating a biomolecule fragment from the biomolecule; b) binding a plurality of uniform probes to the biomolecule fragment; c) identifying a plurality of binding sites along the biomolecule fragment at which the probes bind to the biomolecule; d) creating a collection of binding signatures for the biomolecule fragment, each binding signature representing a series of distances between binding sites within the fragment; e) grouping the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature; f) for each binding signature in a first cluster, selecting a potential successor binding signature from signature clusters other than the first signature cluster; g) identifying one of the potential successor binding signatures as a successor binding signature; h) repeating steps f) and g) until the successor signature represents a terminal signature, resulting in a sequence of signatures representing at least a portion of the biomolecule.
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14. An apparatus for sequencing a biomolecule, the apparatus comprising:
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a memory for storing code that defines a set of instructions; and a processor for executing the set of instructions to; (i) identify a plurality of binding sites along a fragment of the biomolecule at which a plurality of uniform probes are bound; (ii) create a collection of binding signatures for the fragment, each binding signature representing a series of distances between binding sites within the fragment; (iii) group the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature; (iv) select, for each binding signature in a first cluster, a potential successor binding signature from signature clusters other than the first signature cluster; (v) identify one of the potential successor binding signatures as a successor binding signature; and (vi) determine the sequence of at least a portion of the biomolecule based at least in part on a series of identified successor binding signatures.
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Specification