Insights into transcriptomes of big and low sagebrush

We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.

BamBam: genome sequence analysis tools for biologists

Background

Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results.

Findings

We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments.

Conclusions

BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.

Electronic supplementary material

The online version of this article (doi:10.1186/1756-0500-7-829) contains supplementary material, which is available to authorized users.

BamBam: genome sequence analysis tools for biologists

BACKGROUND

Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results.

FINDINGS

We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments.

CONCLUSIONS

BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.

Suspected acute appendicitis: nonenhanced helical CT in 300 consecutive patients

PURPOSE

To determine the accuracy of helical computed tomography (CT) without the oral, intravenous, or rectal administration of contrast material in confirming suspected acute appendicitis.

MATERIALS AND METHODS

Three hundred consecutive patients referred from the departments of surgery and emergency medicine were examined for suspected acute appendicitis by using thin-section nonenhanced helical CT. All transverse CT scans were obtained in a single breath hold from the upper abdomen (T12 vertebra) to the pubic symphysis with 5-mm collimation and a pitch of 1.6. All scans were obtained without oral, intravenous, or rectal contrast material. Criteria for diagnosis of acute appendicitis included an enlarged appendix (> 6 mm) and periappendiceal inflammation. CT diagnoses were recorded prospectively. Final diagnoses were established with the results of surgical or clinical follow-up or both.

RESULTS

There were 110 true-positive diagnoses, 181 true-negative diagnoses (63 of which were an alternative diagnosis correctly established prospectively), five false-negative diagnoses, and four false-positive diagnoses, which yielded a sensitivity of 96%, a specificity of 99%, and an accuracy of 97%.

CONCLUSION

Nonenhanced helical CT is a highly accurate technique for diagnosing or excluding acute appendicitis. Developing experience with the technique and understanding the subtleties of interpretation can further improve diagnostic accuracy.