Systems and methods for biopolymeric probe design using graphical representation of a biopolymeric sequence

Abstract

Systems and methods for using the same to obtairi one or more probe sequences in response to an input graphical representation of a biopolymeric sequence are provided. Also provided are computer program products for executing the subject methods.

Description

BRIEF DESCRIPTIONS OF THE DRAWINGS

FIG. 1 illustrates a substrate carrying multiple arrays, such as may be fabricated by methods of the present invention;

FIG. 2 is an enlarged view of a portion of FIG. 1 showing multiple ideal spots or features;

FIG. 3 is an enlarged illustration of a portion of the substrate in FIG. 2;

FIG. 4 schematically illustrates a representative system of the present invention;

FIG. 5 provides a functional block diagram for a graphics-based probe obtainment method according to an embodiment of the present invention;

Claims

1. A system for obtaining at least one probe corresponding to a selected region of a biopolymeric sequence, said system comprising: (a) an input manager for receiving a user biopolymer request, wherein said user biopolymer request comprises a graphical representation of a biopolymeric sequence;(b) a probe developer for obtaining at least one probe corresponding to a selected region of said graphical representation of said biopolymeric sequence;(c) an output manager for providing said at least one obtained probe.

2. The system according to claim 1, wherein said system further comprises a graphical user interface (GUI) for transferring information between said system and a user.

3. The system according to claim 1, wherein said system further comprises a graphics developer for generating at least one graphical representation of a biopolymeric sequence in-response to identifier of said sequence.

4. The system according to claim 3, wherein said graphics developer is configured to generate graphical representations that can be manipulated by a user.

5. The system according to claim 3, wherein said graphics developer is configured to automatically update said graphical representation of said biopolymeric sequence in response to a user selecting a region of said graphical representation of said biopolymeric sequence.

6. The system according to claim 1, wherein said probe developer is configured to obtain said probe by using a probe design algorithm.

7. The system according to claim 1, wherein said probe developer is configured to obtain said probe by retrieving a probe from a database.

8. The system according to claim 1, wherein said output manager further provides probe content and associated annotation information relating to said at least one probe corresponding to said selected region.

9. The system according to claim 1, wherein said system provides for remote communication between a user and said system.

10. The system according to claim 1, wherein said system provides for communication between a user and said system via the Internet.

11. The system according to claim 1, wherein said system obtains a group of probe sequences corresponding to said selected region.

12. The system according to claim 11, wherein said system obtains a plurality of probe groups corresponding to said selected region.

13. The system according to claim 1, wherein said output manager provides said user with an option to select for purchase one or more of said obtained probes.

14. The system according to claim 13, wherein in response to said purchasing the one or more probe sequences are synthesized on an array.

15. A method for obtaining at least one probe corresponding to a selected region of a biopolymeric sequence, said method comprising: (a) submitting a biopolymer request to a system according to claim 1, wherein said biopolymer request comprises a graphical representation of a biopolymeric sequence; and(b) obtaining at least one probe from said system in response to said request.

16. The method according to claim 15, wherein said method further comprises viewing at least one graphical representation of said biopolymeric sequence and selecting at least one region of said graphical representation.

17. The method according to claim 15, wherein said biopolymeric sequence is a nucleic acid sequence.

18. The method according to claim 17, wherein said nucleic acid is at least a part of a chromosome.

19. The method according to claim 15, wherein said biopolymeric sequence is an amino acid sequence.

20. The method according to claim 15, wherein said probe is a nucleic acid.

21. The method according to claim 15, wherein said probe is a polypeptide.

22. The method according to claim 15, wherein said region is selected by highlighting said region on said graphical representation of said nucleic acid.

23. The method according to claim 15, wherein said graphical representation is manipulatable.

24. The method according to claim 22, wherein said highlighted region is represented as a distinct graphical representation from said graphical representation of said nucleic acid.

25. The method according to claim 24, wherein said distinct graphical representation is a distinct color.

26. The method according to claim 15, wherein said obtaining step comprises submitting said selected region to a nucleic acid probe database.

27. The method according to claim 15, wherein said obtaining step comprises submitting said selected region to a nucleic acid probe design algorithm.

28. The method according to claim 15, wherein said submitting is via the Internet.

29. The method according to claim 13, wherein any of said steps are reiterated.

30. The method according to claim 15, further comprising selecting at least one of said obtained probes and saving it in a database.

31. The method according to claim 30, further comprising adding probes to said database.

32. The method according to claim 30, further comprising deleting probes from said database.

33. The method according to claim 30, wherein probes obtained from different selected regions are added to said database.

34. The method according to claim 15, wherein multiple regions of said biopolymeric sequence are selected on said graphical representation.

35. The method according to claim 16, wherein the binding location of said at least one probe is indicated graphically on said graphical representation of said selected region.

36. A method for obtaining at least one probe corresponding to a selected region of a biopolymeric sequence, said method comprising: (a) receiving a biopolymer request that comprises a graphical representation of a biopolymeric sequence; and(b) obtaining at least one probe in response to said request.

37. A computer program product comprising a computer readable storage medium having a computer program stored thereon, wherein said computer program, when loaded onto a computer, operates said computer to: a) receive a biopolymer request that comprises a graphical representation of a biopolymeric sequence; andb) obtain at least one probe in response to said request.