Computer systems for annotation of single molecule fragments

• US 9,396,304 B2
• Filed: 07/12/2004
• Issued: 07/19/2016
• Est. Priority Date: 07/10/2003
• Status: Active Grant

• Current Assignee: Wisconsin Alumni Research Foundation (University of Wisconsin System)
• Original Assignee: Wisconsin Alumni Research Foundation (University of Wisconsin System)
• Inventors: Schwartz, David Charles, Severin, Jessica
• Primary Examiner(s): NEGIN, RUSSELL SCOTT
• Application Number:
  US10/888,517
• Publication Number:
  US 20120249580A1
• Time in Patent Office: 4,390 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: G09F 19/16 involving the use of mirrors
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations

Abstract

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Claims

1. A computer system communicatively linked to a database storing single molecule image data and corresponding identifying data, the computer system programmed to:

selectively retrieve at least two single molecule image data from the database wherein each single molecule image data depicts a region of a restriction fragment and comprises at least one pixel having image and intensity level data, and wherein the single molecule image data each include at least one pixel representing an overlapping region of the same single molecule image;

calculate an average intensity level for at least one of the single molecule image data retrieved from the database by averaging an intensity level of each pixel of the at least one single molecule image data;

display the at least two single molecule image data retrieved from the database on a user interface;

display the intensity level for each pixel of the at least two single molecule image data retrieved from the database on the user interface;

differentiate at least one restriction fragment in the single molecule image data from a background in the single molecule image data by applying an intensity level threshold analysis to each pixel of the single molecule image data;

magnify each of the at least one restriction fragments for display on the user interface;

form a collage by aligning the overlapping regions of the at least two single molecule image data;

generate a linear representation of the restriction fragments by;

(a) receiving an input signal from a marking tool provided to a user, the input signal indicating a point on the user interface associated with a pixel of the single molecule image data;

(b) repeating step (a) to define successive points in a single restriction fragment;

(c) retrieving the single molecule image data associated with points between each successive point; and

(d) storing the retrieved single molecule image data as the single restriction fragment;

associate the restriction fragments;

order the associated restriction fragments based on their relative positions; and

store the ordered restriction fragments as a restriction map in a file adapted for use in map generation.

2. The computer system of claim 1, further programmed to visually distinguish the at least two restriction fragments displayed on the user interface.

3. The computer system of claim 1, wherein the database is an object database.

4. The computer system of claim 1, wherein the single molecule image data is derived from optical signals derived from atomic force microscopy.

5. The computer system of claim 1, wherein the restriction fragment is displayed on the user interface as a generally contiguous region of the single molecule image data having an intensity level greater than the intensity level threshold.

6. The computer system of claim 1, further programmed to display a backbone mark-up on the user interface, wherein the backbone mark-up is a graphic overlay comprising lines connecting the successive points.

7. The computer system of claim 6, further programmed to receive an input signal from a marking tool provided to a user indicating a selected restriction fragment to remove from the list of selected restriction fragments.

8. The computer system of claim 1, further programmed to:

receive an input signal from a marking tool provided to a user, the input signal indicating a point within a restriction fragment displayed on the user interface;

select the restriction fragment;

highlight the selected restriction fragment on the user interface;

add the selected restriction fragment to a list of restriction fragments; and

store the selected restriction fragment in a file adapted for use in map generation.

9. The computer system of claim 1, further programmed to receive an input signal from a marking tool provided to a user, the input signal indicating a point of the restriction fragment to add a cut;

and

divide the restriction fragment into a first restriction fragment and a second restriction fragment;

wherein the first restriction fragment ends at the cut and the second restriction fragment starts at the cut.

10. The computer system of claim 1, further programmed to display graphic overlays on the molecule fragments on the user interface;

wherein the graphic overlays contain corresponding identifying data.

11. A computer-implemented method for selecting single restriction fragments from single molecule image data, wherein the single molecule image data comprises pixels having image and intensity data, the computer-implemented method comprising the steps of:

obtaining the single molecule image data from a database;

wherein the single molecule data depicts a region of a restriction fragment and comprises at least one pixel;

calculating an intensity level for each pixel of the single molecule image data;

calculating an average threshold intensity of the single molecule image data;

displaying a portion of the single molecule image data using a user interface;

marking each pixel of the single molecule image data having a threshold intensity level greater than the average threshold intensity as a pixel of a restriction fragment image on the user interface;

receiving an input signal from a marking tool provided to a user via the user interface, the input signal identifying one or more pixels of the single molecule image data;

scaling a magnification of the restriction fragment for display on the user interface;

forming a single restriction fragment from a plurality of contiguous pixels of the single molecule image data, the plurality of contiguous pixels of the restriction fragment image including a pixel identified by the user input;

displaying the restriction fragment via the user interface; and

storing the restriction fragment in the database in a form adapted for use in map generation.

12. The method of claim 11, wherein the step of marking further comprises receiving at least two coordinates of pixels in the single molecule image data and marking all of pixels in a generally linear direction between the coordinates as pixels of a restriction fragment image.

13. The method of claim 11, further comprising the step of joining two or more molecule fragment images into a single molecule image comprising the steps of:

generating linear representations of each restriction fragment image;

associating two or more restriction fragment images;

ordering the two or more restriction fragment images based on their relative positions; and

storing the ordered restriction fragment images as a restriction map.