Recursive categorical sequence assembly
First Claim
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1. A method for creating an assembly comprising:
- (a) obtaining a set of DNA or RNA sequence reads;
(b) grouping the DNA or RNA sequence reads into categories;
(c) running an assembly program on each of the separate categories of DNA or RNA sequence reads; and
(d) repeating steps (b) and (c) as necessary.
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Abstract
The present invention provides a method for efficiently creating assemblies. The present invention also provides a web-based system for scientists to interact with a computer to implement the method. Further the scientist is able to upload and download information to and from the method to and from a database. The present invention also provides an efficient hardware architecture to implement the method.
27 Citations
25 Claims
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1. A method for creating an assembly comprising:
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(a) obtaining a set of DNA or RNA sequence reads;
(b) grouping the DNA or RNA sequence reads into categories;
(c) running an assembly program on each of the separate categories of DNA or RNA sequence reads; and
(d) repeating steps (b) and (c) as necessary. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. An apparatus for creating assemblies from DNA or RNA sequence reads comprising:
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(a) means for obtaining a set of DNA or RNA sequence reads;
(b) means for grouping DNA or RNA sequence reads into categories; and
(c) means for creating assemblies from the DNA or RNA sequence reads.
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13. In a computer system having a graphical interface including a display device and a selection device, a method of displaying information on the display device in a menu form and accepting menu selection input from a user, the method comprising:
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retrieving a set of menu entries for the menu, each of the menu entries representing a method to perform upon DNA or RNA sequence reads;
displaying the set of menu entries on the display device;
displaying a set of parameters on the display device;
providing the user an opportunity to modify said set of parameters;
receiving an indication of a menu entry selection from the user via the selection device; and
in response to said indication of a menu entry selection, performing a method on'"'"'the DNA or RNA sequence reads to create assemblies based on said set of parameters and said set of menu entries.
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14. A set of application program interfaces embodied on a computer-readable medium for execution on a computer in conjunction with an application program that determines assemblies of DNA or RNA sequence reads, comprising:
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a first interface that receives functions for a method for assembling DNA or RNA sequence reads;
a second interface that receives parameters for said functions;
a third interface that receives DNA or RNA sequence reads; and
returns an assembly of said DNA or RNA sequence reads.
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15. A method for assembling sequence reads, comprising the steps of:
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a) categorizing a plurality of sequence reads into at least two sub-groups of sequence reads based on an identifiable characteristic of the sequence reads in each sub-group;
b) matching sequences reads within each sub-group thereby creating assemblies of said sequence reads within each respective sub-group; and
c) repeating steps a) and b) with all unassembled sequence reads and newly created assemblies. - View Dependent Claims (16, 17, 18, 19, 20, 21, 22, 23, 24, 25)
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Specification