Computer-assisted recombinant DNA design and analysis with Matilda

Abstract

Abstract Creating a recombinant DNA usually involves two phases of analysis. Functional sites (e.g. boundaries of coding regions, intrans, promoters, etc.) and restriction sites are mapped in the first phase, usually both by experimentation and by DNA sequence analysis. The functional and restriction site maps that are produced in this phase are used to devise the recombination strategy in the second phase. The distinction between the two phases of analysis is apparent in the different ‘languages’ that are used. While sequences, restriction enzyme patterns, and consensus sequences are described using the four-letter nucleotide code, DNA fragments and recombinant clones are described using restriction enzyme names and locations, functional information, and descriptions of the boundaries and ancestries of DNA segments in a clone (which regions came from pBR322, for instance). Many software packages are available that provide the variety of DNA sequence analysis procedures applicable to the first phase (homology searching, translation, secondary structure prediction, etc.) (1). However, these programs do not, in general, directly address the problems of the second phase. These are usually described, and best solved, in terms of the higher-level language of restriction and functional site maps, not in terms of nucleotide sequence. This is particularly true for cloning operations with DNAs that have only been partially sequenced and where additional experimental data is important.