Researchers demands for publication-quality graphic products have fueled development of plasmid mapping software (Gene Construction Kit, NetPlasmid, PDRAW32, REMAP, SimVector, and Visual Cloning) and it is this function that has seen considerable development. Though identification of restriction sites from sequences is still important for vector construction, online tools (In Silico Restriction Cutting, NEB Cutter, WatCut), freebies (EnzymeX), and integrated products mentioned above satisfy these needs well. Restriction enzyme related software is another category whose original usefulness has paled in comparison to bigger project demands and has expanded to meet new needs. Offerings here include CAP3, iCE, MERGER, MIRA2, Paracel Genome Assembler, Paracel Transcript Assembler, and Sequencher.Ī few tools for sequence manipulation, such as translating, reverse complementing, and inverting are still out there (Reverse Complement), but this subcategory serves as little more than a reminder of computational problems of long ago. The third is for assembly of contigs generated by sequencing projects. The second is the development of software to read automated sequence information (4Peaks, ABI View, PHRED, TraceTuner). A few products meet those needs (biOpen, CINEMA, ElDorado, STING). The first is the desire of users to format sequences with color, annotations, and other information. The category of sequence display/editing/manipulation has expanded considerably in recent years as demands peripheral to simple sequence editing have arisen from genome projects. MacVector users rejoiced in the release of a new version (8.0) designed to take advantage of OS X, breathing life into Bill Kraus original standard that keeps plugging along. The past couple of years have witnessed one commercial product resurrected from the dead (DNASIS), and one collection suffering from neglect (ChromaTool, GeneTool, and PepTool), as well as expansion (LaserGene), and new ownership (Vector NTI Suite, acquired by Invitrogen). Despite inroads being made by the open source movement, commercial vendors appear to be holding on, at least as measured by their numbers. The category of integrated software products has grown in number with a couple of new additions (DNAssist and Sequence Manipulation Suite). Microarrays have provided very fertile programming problems, with software products that assist in almost every aspect of array-related research, from design to visualization to statistical analysis to integration of information to system-wide understanding.
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