Method and apparatus for extracting attributes from sequence strings and biopolymer material

• US 6,898,530 B1
• Filed: 09/30/1999
• Issued: 05/24/2005
• Est. Priority Date: 09/30/1999
• Status: Expired due to Term

• Current Assignee: Battelle Memorial Institute
• Original Assignee: Battelle Memorial Institute
• Inventors: Monroe, Philip J., Chen, Guang, Calapristi, Augustin J., Saffer, Jeffrey D., Sofia, Heidi J., Miller, Nancy E., Scarberry, Randall E., Stillwell, Lisa C.
• Primary Examiner(s): Allen, Marianne P.
• Assistant Examiner(s): Mahatan, Channing S.
• Application Number:
  US09/409,260
• Time in Patent Office: 2,063 Days
• Field of Search: 702/20, 702/19
• US Class Current: 702/19
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

Systems for creating high-dimensional vectors representing sequence strings and biopolymer materials are provided. A first system for divides respective sequence strings into blocks of at least three units to create a vocabulary of blocks. A second system selects predefined domains of a plurality of items of biopolymer materials. A third system defines each item of biopolymer material in a data set of biopolymer materials as a surface using descriptors of at least one of structure and function. A fourth system compares information regarding each biopolymer material of a plurality of biopolymer materials to information regarding each other biopolymer material.

Claims

1. A method of visualizing comparison results for at least one of a plurality of biopolymer materials represented in a set of sequences, the method comprising:

comparing a sequence of each biopolymer material to a sequence of each other biopolymer material to provide respective comparison results;

arranging the comparison results in a square matrix indexed by the plurality of biopolymer materials;

creating a high-dimensional context vector for at least one of the biopolymer materials based on a row or column of the square matrix; and

projecting the context vector onto a two- or three-dimensional viewing area;

thereby visualizing comparison results for at least one of a plurality of biopolymer materials represented in the set of sequence.

2. The method according to claim 1, wherein from each row or column of the square matrix, a respective high-dimensional context vector is created for each of the biopolymer materials based on the comparison results in the row or column.

3. The method according to claim 1, wherein the comparing uses a Basic Local Alignment Search Tool.

4. The method according to claim 1, wherein the comparing provides comparison results based on an expectation of a relation.

5. The method according to claim 1, wherein the biopolymer material is protein.

6. The method according to claim 1, wherein the biopolymer material is nucleic acid.

7. The method of claim 1, wherein the context vector is utilized for comparison of the biopolymer materials using cluster analysis.

8. The method of claim 1, wherein the context vector comprises a row or column of an object attribute matrix of comparison results.

9. An apparatus for visualizing comparison results for at least one of a plurality of biopolymer materials represented in a set of sequences, the apparatus comprising:

at least one memory having program instructions,

at least one computer output device for visualizing comparison results, and

at least one processor configured to execute the program instructions to perform the operations of;

comparing a sequence of each biopolymer material to a sequence of each other biopolymer material to provide respective comparison results;

arranging the comparison results in a square matrix indexed by the plurality of biopolymer materials;

creating a high-dimensional context vector for at least one of the biopolymer materials based on a row or column of the square matrix; and

projecting the context vector onto a two- or three-dimensional viewing area,

wherein the apparatus enables visualization of the comparison results for the respective biopolymer material.

10. A computer-readable medium containing instructions for controlling a computer system to perform a method for visualizing comparison results for at least one of a plurality of biopolymer materials represented in a set of sequences, the method comprising:

comparing a sequence of each biopolymer material to a sequence of each other biopolymer material to provide respective comparison results;

arranging the comparison results in a square matrix indexed by the plurality of biopolymer materials;

creating a high-dimensional context vector for at least one of the biopolymer materials based on a row or column of the square matrix; and

projecting the context vector onto a two- or three-dimensional viewing area,

wherein the method enables visualization of the comparison results for the respective biopolymer material.