CABIOS COMMUNICATION Vol. 11 no. 3 1995 Pages 331-335 DNASUN: a package of computer programs for the biotechnology laboratory A.A.Mironov 1 , N.N.AIexandrov 1 ' 2 , N.Yu.Bogodarova 1 , A.Grigorjev 1 ' 3 , V.F.Lebedev 1 , L.V.Lunovskaya 1 , M.E.Truchan 1 and P.A.Pevzner 1 ' 4 Abstract The paper describes a new software package DNASUN developed for supporting gene engineering laboratories. The package provides a user-friendly interface for experimental researches and supports the traditional nucleotidejprotein sequence analysis as well as physical mapping, sequencing, plasmid manipulations, optimal oligonucleotide probe selection and other common molecular biology procedures. Introduction Molecular biologists encounter significant difficulties trying to obtain DNA sequences and to derive biologi- cally significant information from these data. Numerous molecular biology software tools developed mainly by computer scientists are often found unsatisfactory by biologists. To eliminate a cultural gap between computer scientists and biologists DNASUN has been implemented in the biological environment; the modules of DNASUN have been extensively tested in the biological laboratories and numerous recommendations of biologists have been taken into consideration. The DNASUN user-friendly interface and every-day-use programs have been develop- ing since 1986 in a close collaboration with gene engeneers. Besides every-day-use programs DNASUN contains some programs which are still rare in the general purpose molecular biology software. DNASUN (version 3.30) has been implemented on IBM PC/AT/PS2 microcomputers (640 Kb memory and 4 Mb hard disk space are required) using Microsoft C (version 5.1) and Microsoft MacroAssembler (version 5.1) (Microsoft is the registered trademark of Microsoft Corporation). The CGA, MGA, EGA, VGA, Hercules videoadapters are supported. DNASUN runs under MS DOS 3.00 (or later versions) and under MS Windows as DOS background application. The running time in the examples below is given for 40 MHz IBM PC/AT-386 (hard disk with random access time 17 ms). DNASUN (version 3.30) is available by contacting A.A.M. for the nominal cost covering shipping, copying and English translation of the manual. All software components of DNASUN run by the management program under the same name. DNASUN has specialized menu manager and hypertext electronic manual directed towards molecular biology applications. This menu manager allows an apply programmer and even an user to customize a dialogue stream conveniently. DNASUN has his own file manager and user-directed options for viewing, analyzing and printing the results. All programs are supplied with on-line helps and descriptions. If necessary, a user can adjust help windows for his own purposes and even add additional help windows depend- ing on personal convenience. DNASUN is an open package; it can be readily extended by new programs. DNASUN 3.30 contains about 400 menu items, 45 executable modules and provides, in particular, the following functions • Electroforegrams/gels/sequences input • DNA and protein sequence editing • DNA and protein database manager • Dot-matrices construction • Pairwise sequence alignment • Motif search • Multiple sequence alignment • Fast database search • DNA statistics • RNA secondary structure • Plasmid manager • Optimal oligonucleotide probe selection • Small-scale DNA physical mapping • DNA sequencing The software implementations are based on the algorithms developed by the authors and described in more than 40 papers published in 1986-1994 and in the book Alexan- drov el al., 1990. 'Laboratory of Mathematical Methods, National Centerfor Biotechnology NIIGENETIKA, Moscow 113545, Russia, 'National Cancer Institute, Frederick, MD 21702, USA. imperial Cancer Research Fund, 44 Lincoln's Inn Fields, London WC2A 3PX, UK and 4 Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA General description of the package Electroforegrams/gels/'sequences input DNASUN facilitates the input of nucleotide and amino acid sequences and supports various instruments for gels ) Oxford University Press 331