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Nucleic Acids Research, 1982, Vol. 10, No. 1 305-321
© 1982

Articles

GEL, a DNA sequencing project management system

Jan Clayton1 and Larry Kedes2,

1IntelliGenetics, Inc. 124 University Avenue, palo Alto, CA 94301 2Departments of Medicine, Stanford University and Veterans Administration medical Center Palo Alto, CA 94304, USA

Address all correspondence to: Dr.L.H.Kedes, 151M, VA Hospital, Miranda Avenue, Palo Alto, CA 94304, USA

Received September 15, 1981. We have developed an automated system for management of DNA sequencing projects. The system, named GEL, can handle data from both random sequences and from fragments whose relative positions are known. The system is highly interactive, self-documenting, and forgiving; it is designed for use by computer-naive molecular biologists. An editor designed specifically for sequences allows simple entry of data. Special functions allow direct checking and immediate editing of paired readings of the same gel. Merging of new random fragment sequences into the project as a whole is semi-automated. The user is shown probable overlaps if they exist, and can edit either the sequences or the consensus. Heuristic approaches to limiting the kinds of searches made in the merging process reduces the problem of combinatonc data overload as sequencing projects grow large. Complete histories of all entries, editing changes, and generation of consensus sequences are automatically prepared.


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