Recursive categorical sequence assembly
OwnerMichael Wallinventor
Life of this patent
Estimating the term…
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.
Claims25
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.
An apparatus for creating assemblies from DNA or RNA sequence reads comprising:
- (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.
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:
- 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.
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:
- 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.
A method for assembling sequence reads, comprising the steps of:
- 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.
Dependencies are inferred from the claim text.