Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Gel Analysis Programs for 'DOG' and STS Content Mapping

S. Pitluck, K. Gong, S. Lewis
Human Genome Informatics Group, Lawrence Berkeley Laboratory, Berkeley, CA 94720

A gel analysis program (Angel) originally developed to analyze restriction gels, has been adapted for the production of maps related to the LBL Directed Sequencing Strategy. This program automatically detects gel lanes and locates and sizes bands in the lanes. In order to adapt Angel for other tasks and simplify even the current minimal user interaction, more specific versions of Angel were created. These special versions also contain several enhancements.

One of the first modifications to Angel allows the operator to use a slide bar to vary the contrast of the displayed image. Another enhancement is the automatic display of both the normal gel lanes as well as the special marker lanes. Another slide bar is available to adjust the location of these overlayed lane markings. Moving the mouse up and down within a marker lane also moves a horizontal line up and down across the image. This is useful for aligning various bands. If the gel image is being used for STS mapping, then clicking the mouse button on any bands outside the marker lanes will result in the recording of the original microtiter plate or row/column locations for that clone. This information is used to determine which P1 was hit by the particular STS. Thus by just pointing and clicking, many images can be rapidly analyzed. In addition, the relevant derived information is saved as a ".ace" file for inclusion in our database. Images can be reexamined at a later date while using the database. Band selections made earlier will then be automatically redisplayed, and revisions to the analysis are supported.

Another version of the software (DAngel) has been created to assist in our Directed Sequencing strategy. For the specific purposes of mapping the 3kb fragments called 'DOGS', the program records the band sizes based on the reference markers, as well as "de-pooling" the clone to identify its microtiter plate location.

In terms of performance, Research Technicians using these programs estimate that processing time has dropped by a factor of about 3 to 5, compared with the largely manual way in which these analyses were performed previously. More important, perhaps, is the reduction in the number of human errors, due to automatic data capture.