ABSTRACT
The integration of software into special-purpose systems (e.g. for gene sequence analysis) can be a difficult task. We describe a general-purpose software integration tool, the BCE program, that facilitates assembly of VAX-based software into application systems and provides an easy-to-use, intuitive user interface. We describe the use of BCE to integrate a heterogeneous collection of sequence analysis tools. Many BCE design features are generally applicable and can be implemented in other language or hardware environments.
Subject(s)
Software , Algorithms , Biotechnology/methods , Software DesignABSTRACT
We describe computer programs that predict the most energetically favorable secondary structures in growing RNA sequences, generate a sequential display of the growing structures, and monitor the predicted participation of intramolecular sites in secondary structure. These programs may provide insight into the relationships between messenger RNA secondary structure and expressibility.
Subject(s)
Nucleic Acid Conformation , RNA, Messenger , Software , Algorithms , Models, Molecular , ThermodynamicsABSTRACT
We describe an interactive computational tool, GENEVIEW, that allows the scientist to retrieve, analyze, display and exchange genetic information. The scientist may request a display of information from a GenBank locus, request that a restriction map be computed, stored and superimposed on GenBank information, and interactively view this information. GENEVIEW provides an interface between the GenBank data base and the programs of the Lilly DNA Computing Environment (DNACE). This interface stores genetic information in a simple, free format that has become the universal convention of DNACE; this format will serve as the convention for all future software development at Eli Lilly and Company, and could serve as a convention for genetic information exchange.
Subject(s)
Computers , Information Systems , Nucleic Acids/analysis , Software , Animals , Base Sequence , Cattle , Enkephalin, Methionine/genetics , Enkephalins/genetics , Protein Precursors/geneticsABSTRACT
We describe an interactive computational tool, PLASMAP, which allows the user to electronically store, retrieve, and display circular restriction maps. PLASMAP permits users to construct libraries of plasmid restriction maps as a set of files which may be edited in the laboratory at any time. The display feature of PLASMAP quickly generates device-independent, artist-quality, full-color or monochrome, hard copies or CRT screens of complex, conventional circular restriction maps.
Subject(s)
Base Sequence , Computers , DNA Restriction Enzymes , Minicomputers , Plasmids , Software , Cloning, Molecular , DNA/genetics , Genes , Models, GeneticSubject(s)
Computers , Genetic Engineering , Information Systems/instrumentation , Amino Acid Sequence , Base Sequence , Communication , Data Display , SoftwareABSTRACT
I have tried to describe why the computer is an essential tool for the recombinant DNA scientist. As our data bases grow, we will require information storage and communication systems unlike the paper based record systems with which we currently work. Molecular biological data is being generated so rapidly that I believe electronic data exchange will soon be the only way we will be able to keep each other up to date. We have seen some specific computer applications which provide assistance to the researcher at the bench. Sequence manipulation, analysis, and display are too difficult for the unaided molecular biologist to accomplish readily. The computer, being able to provide intelligence at speeds unmatchable by humans, will continue to be used as a tool in recombinant DNA research and will rapidly grow to be an essential tool for all scientists.
