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Context Reusing software by means of copy and paste is a frequent activity in software development. The duplicated code is known as a software clone and the activity is known as code cloning. Software clones may lead to bug propagation and serious maintenance problems. Objective This study reports an extensive systematic literature review of software clones in general and software clone detection in particular. Method We used the standard systematic literature review method based on a comprehensive set of 213 articles from a total of 2039 articles published in 11 leading journals and 37 premier conferences and workshops. Results Existing literature about software clones is classified broadly into different categories. The importance of semantic clone detection and model based clone detection led to different classifications. Empirical evaluation of clone detection tools/techniques is presented. Clone management, its benefits and cross cutting nature is reported. Number of studies pertaining to nine different types of clones is reported. Thirteen intermediate representations and 24 match detection techniques are reported. Conclusion We call for an increased awareness of the potential benefits of software clone management, and identify the need to develop semantic and model clone detection techniques. Recommendations are given for future research.

Applications that use Bacterial Artificial Chromosome (BAC) libraries often require paired-end sequences and knowledge of the physical location of each clone in plates. To facilitate obtaining this information in high-throughput, we generated pBACode vectors: a pool of BAC cloning vectors, each with a pair of random barcodes flanking its cloning site. In a pBACode BAC library, the BAC ends and their linked barcodes can be sequenced in bulk. Barcode pairs are determined by sequencing the empty pBACode vectors, which allows BAC ends to be paired according to their barcodes. For physical clone mapping, the barcodes are used as unique markers for their linked genomic sequence. After multi-dimensional pooling of BAC clones, the barcodes are sequenced and deconvoluted to locate each clone. We generated a pBACode library of 94,464 clones for the flounder Paralichthys olivaceus and obtained paired-end sequence from 95.4% of the clones. Incorporating BAC paired-ends into the genome preassembly improved its continuity by over 10-fold. Furthermore, we were able to use the barcodes to map the physical locations of each clone in just 50 pools, with up to 11 808 clones per pool. Our physical clone mapping located 90.2% of BAC clones, enabling targeted characterization of chromosomal rearrangements.

Clone detection finds application in many software engineering activities such as comprehension and refactoring. However, the confounding configuration choice problem poses a widely-acknowledged threat to the validity of previous empirical analyses. We introduce desktop and parallelised cloud-deployed versions of a search based solution that finds suitable configurations for empirical studies. We evaluate our approach on 6 widely used clone detection tools applied to the Bellon suite of 8 subject systems. Our evaluation reports the results of 9.3 million total executions of a clone tool; the largest study yet reported. Our approach finds significantly better configurations (p

The public project's sequencing strategy involved producing a map of the human genome, and then pinning sequence to it. This helps to avoid errors in the sequence, especially in repetitive regions.

The sequence of nucleotides within a DNA molecule can yield a wealth of information. Important biological features such as amino acid sequence, exact amino acid composition, and gene structure are contained within sequences. The data can be used for highly specific manipulations of cloned DNA, such as changing a single nucleotide, substituting promoters between genes, and fusing of genes to yield hybrid (heterologous) proteins. Probes can also be designed for a variety of uses, including the detection of genetic diseases and pathogenic microbes.

Products for recombinant DNA studies described this week include a biotin clone detection kit and a system for dissecting yeast asci.

M y review copy of David Rorvik's sensational account of the first human clone bore three identical dust jackets. The problematic relationship between the nominally scientific subject of the book and its decidedly unscientific manner of publication was thus unexpectedly highlighted for me even before I could begin reading it. Was this an abnormality in the book's reproduction or one more inspired touch in its marketing, like the imaginative use of an Escher engraving -two hands each drawing the other-to grace the book jacket? I confess to a pang of disappointment on discovering that other bookstore copies had come into the world with only the usual single protective amnion. The actual text provided another surprise. I had frankly expected to find a crude hoax whose numerous and glaring scientific errors could be tallied up in a spirit of how-many-mistakes-can-youspot. As it turns out, Rorvik's account is a much more challenging puzzle. As a former science writer for Time and the author of several less-controversial books on the promises and perils of the biological revolution, Rorvik has acquired an extensive knowledge of current research in biology and medicine; and he has used it to good effect. In the presentation of the scientific background there are some technical inaccuracies, but no absurdities, and any misconceptions are subtle rather than egregious. The discussions of technical procedures involving micromanipulation of cells, cellular fusions, test-tube fertilizations, and embryo transfers constitute quite a lucid explanation of some very complex research protocols. If this book had addressed itself to the topic of likely research developments on the way to cloning the first Guernsey cow-without going so far as claiming that this feat had already been achieved in secret at a private bovine research station on Tierra del FuegoRorvik would have received few, if any, barrages from the scientific community. Of course, such an account would not have raised an exceptional amount of interest or been likely to sell very well. The book Rorvik did write is well on its way to accomplishing both those endsnot because it is a crude hoax, but because it is a sophisticated one. In fact, a comparison of Rorvik's account with some previous examples of the scientific hoax may be the best way of understanding the nature and significance of this current claim on our belief.