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This Week in Nucleic Acids Research: Aug 22, 2012

In Nucleic Acid Research, researchers from City of Hope report on their development of a method to detect the mutational fingerprints of carcinogens, which they then applied to the study of three carcinogens: ultraviolet radiation from the sun, 4-aminobiphenyl, and secondhand smoke. Their approach combines Stratagene's Big Blue mouse mutation detection assay with Roche/454's Genome Sequencer FLX Titanium next-generation sequencing technology and a bioinformatic pipeline. With it, the researchers found that the UV mutational fingerprint contained many G:C→A:T transitions, the 44-aminobiphenyl mutational fingerprint had many G:C→T:A transversions, and the smoke mutational fingerprint was characterized by G:C→A:T transitions, findings that are in concordance with the conventional low-throughput approach. "Our overall findings show that the new method is superior to the conventional method for establishing the mutational fingerprint of carcinogens," the researchers write. "Most importantly, the new method offers great advantages over the traditional method as it saves significant amounts of time, labor, and cost."

In an online advance article in Nucleic Acids Research, investigators in Japan say that they have created a simplified, artificial genetic code — that is made up of less than 20 amino acids. "We first removed specific amino acids from the E. coli S30 cell-free reaction mixture, to eliminate the targeted endogenous translation pathways connecting the specific amino acids and the codons. We then added the tRNA variant with the altered anticodon loop, to reassign Ala or Ser to the unassigned codons," the researchers write. They then found that protein synthesis based on their code was comparable to that based on the universal code. The researchers add that their code will enable the experimental study of protein evolution.

Finally, Daniel Jones from Washington University in St. Louis and his colleagues present a compression algorithm, called Quip, in Nucleic Acids Research. Quip is an open-source, lossless compression algorithm that can be used on FASTQ and SAM/BAM files. They add that, compared with Cramtools, another published and freely-available reference-based compressor, Quip produces a smaller file size even though it keep read identifiers that Cramtools does not. Further, they add that Quip uses less memory, has a similar run time, and is more flexible, though they do note that Cramtools does provide some lossy methods that Quip does not. "Combining reference-based and assembly-based techniques, with carefully tuned statistical compression, the algorithm presented in Quip probes the limit to which NGS data can be compressed losslessly, yet remains efficient enough be a practical tool when coping with the deluge of data that biology research is now presented with," Jones et al. write.