BackgroundBioinformatics software quality assurance is essential in genomic medicine. Systematic verification and validation of bioinformatics software is difficult because it is often not possible to obtain a realistic "gold standard" for systematic evaluation. Here we apply a technique that originates from the software testing literature, namely Metamorphic Testing (MT), to systematically test three widely used short-read sequence alignment programs.ResultsMT alleviates the problems associated with the lack of gold standard by checking that the results from multiple executions of a program satisfy a set of expected or desirable properties that can be derived from the software specification or user expectations. We tested BWA, Bowtie and Bowtie2 using simulated data and one HapMap dataset. It is interesting to observe that multiple executions of the same aligner using slightly modified input FASTQ sequence file, such as after randomly re-ordering of the reads, may affect alignment results. Furthermore, we found that the list of variant calls can be affected unless strict quality control is applied during variant calling.ConclusionThorough testing of bioinformatics software is important in delivering clinical genomic medicine. This paper demonstrates a different framework to test a program that involves checking its properties, thus greatly expanding the number and repertoire of test cases we can apply in practice.

Jumbo squid was very similar to Japanese common squid in terms of myofibrillar Ca2+‐, Mg2+‐ and K+(EDTA)‐ATPase activities. Myofibrils of jumbo squid were significantly stabilized upon addition of Ca2+ and destabilized by increasing KCl concentration for heating. Incubation of muscle homogenate of jumbo squid induced a selective cleavage of myosin into two major fragments and the cleavage was inhibited by EDTA. Autolysis was prominent at and above 0.3 M NaCl where myosin filaments dissolve. The enzyme involved in the autolysis was proved to be unstable showing maximal autolysis rate at 25°C. Washing the homogenate partially reduced the autolysis activity.

The addition of microbial transglutaminase (MTGase) to salted squid muscle paste greatly strengthened the elasticity of the thermal gel, which was produced by the preferential crosslinking of myosin heavy chains through a two-step heating process that consisted of setting at 40 ∞ C and subsequent heating to 80 ∞ C or 90 ∞ C. Starch increased the breaking strength of thermal squid gels, but decreased the deformation. Thus, the starch-added gels became harder and less elastic. Although, when both MTGase and starch were added to squid muscle paste, the changes in viscoelastisity and myosin cross-linking reaction were similar to those with MTGase alone during setting, the storage and loss moduli of the paste sharply increased with an increase in starch content above 70 ∞ C. Subsequently, the thermal gel texture became more brittle or breakable than gels prepared by setting with MTGase only.

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