December 1994
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6 Reads
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Publications (3)
October 1994
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15 Reads
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15 Citations
Genomics
A new software system designed for use in high-throughput DNA sequencing laboratories is described. The Genome Reconstruction Manager (GRM) was developed from requirements derived from ongoing large-scale DNA sequencing projects. Object-oriented principles were followed in designing the system, and tools supporting object-oriented system development were employed for its implementation. GRM provides several advances in software support for high-throughput DNA sequencing: support for random, directed, and mixed sequencing strategies; a novel system for fragment assembly; a commercial object data-base management system for data storage; a client/server architecture for using network computational servers; and an underlying data model that can evolve to support fully automatic sequence reconstruction. GRM is currently being deployed for production use in high-throughput DNA sequencing projects.
February 1993
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4 Reads
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7 Citations
An object model for genome data at all levels of resolution is described. The model was derived by considering the requirements for representing genome related objects in three application domains: genome maps, large-scale DNA sequencing, and exploring functional information in gene and protein sequences. The methodology used for the object-oriented analysis is also described.
Citations (2)
... These assemblers were developed for the then-standard Sanger sequencing technology. They were effective at retroactive correction of assembly errors, using the long, accurate Sanger read lengths for decision making with regards to variant calls and conflicts in read mate pairs that indicate possible chimeras or rearrangements (Dear and Staden, 1991;Lawrence et al., 1994;Myers, 1995;Bonfield and Whitwham, 2010). ...
- Citing Article
October 1994
Genomics
... partial ordering to cope with uncertainty in the fragments of DNA sequences, but front their short surw,y paper it is not clear how they propose to use them. Honda et al. 11993) proposes an object-oriented data model which is also based on the general idea of linear ordering. One slightly different approach is reported in Graves (1993), who developed a general knowledgebased system based on connection graph and a single order relation. ...
Reference:
Using interval logic for order assembly
- Citing Conference Paper
February 1993