MATILDA version 3.0 (1996) MATILDA - Mapping Accessing Transforming Information about Ligated D n As MATILDA is designed for use on IBM-compatible PCs with dot matrix printers. Matilda is a specialized DNA database management system that helps scientists extract the high-level information that they need for recombinant DNA experiments from a large sequence and genetic information database. In contrast with programs that only analyze DNA sequence data, it also incorporates functional data and restriction map data. Sequence and functional data are extracted from sequence files and from additional information provided by the user. As recombinant DNA clones are constructed, their descriptions are added to the database so that they can be used to describe clones constructed at later steps. Designed by molecular biologists, MATILDA answers specialized queries of the kind that are needed for recombinant DNA design and analysis. For example, a scientist can request lists of restriction enzymes which cleave a DNA near, but not within, a particular gene of interest. Data are presented in five classes of printed formats. By combining sequence, functional and clone construction information in a central database, MATILDA also provides the archival services needed for long- term recombinant DNA laboratory data management. MATILDA's update functions can automatically modify an entire database to correct errors or when new discoveries (e.g., of additional restriction enzymes or functional sites) are made. Since data are entered and retrieved in standard formats, information exchange between different investigators is facilitated. Additional information about MATILDA can be found in Isralewitz, B. and Shalloway, D. (1992), Computer assisted recombinant DNA design and analysis with MATILDA. In Microcomputers in Biochemistry: A Practical Approach. C.F.A. Bryce, ed. (IRL Press, Oxford) pp. 159-188. See also Shalloway, D., and Deering, N.R. (1984). Recombinant DNA data management at the restriction and functional site level. Nucl. Acids Res. 12:739-750. (Reprints can be obtained from Dr. D. Shalloway, dis2@cornell.edu). DOWNLOADING AND INSTALLATION: 1) Download MATILDA.ZIP into the subdirectory where you wish the MATILDA system to be installed (e.g. MATILDA3). Extract the program files using PKUNZIP. 2) INITIALIZATION: From the program directory, enter the command SETMAT This starts the configuration program to initialize the program. IMPORTANT!! This program MUST be run prior to using MATILDA for the first time. SETMAT can be run again if it is ever necessary to change installation parameters (e.g., printer port number). 3) To start MATILDA, change to the program directory and enter MATILDA 4) Program documentation is located in the DOC subdirectory. The enzyme list in ENZLIST.EC is that used in the Shalloway laboratory as of March, 1996. This includes all commercially available restriction enzymes of which we had knowledge; however, most entries with alternate isoschizomers have been commented out.