SummaryWIsH predicts prokaryotic hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. Over the best current tool, WisH shows much improved accuracy on phage sequences of a few kbp length and runs hundreds of times faster, making it suited for metagenomics studies.Availability and implementationOpenMP-parallelized GPL-licensed C ++ code available at .Supplementary information Supplementary data are available at Bioinformatics online.

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The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.

Wheat (Triticum aestivum L.) grain storage proteins (GSPs) are major determinants of flour end-use value. Biological and molecular mechanisms underlying the developmental and nutritional determination of GSP accumulation in cereals are as yet poorly understood. Here we timed the accumulation of GSPs during wheat grain maturation relative to changes in metabolite and transcript pools in different conditions of nitrogen (N) and sulfur (S) availability. We found that the N/S supply ratio modulated the duration of accumulation of S-rich GSPs and the rate of accumulation of S-poor GSPs. These changes are likely to be the result of distinct relationships between N and S allocation, depending on the S content of the GSP. Most developmental and nutritional modifications in GSP synthesis correlated with the abundance of structural gene transcripts. Changes in the expression of transport and metabolism genes altered the concentrations of several free amino acids under variable conditions of N and S supply, and these amino acids seem to be essential in determining GSP expression. The comprehensive data set generated and analyzed here provides insights that will be useful in adapting fertilizer use to variable N and S supply, or for breeding new cultivars with balanced and robust GSP composition.

Use cases are the main requirements vehicle of the UML and are used widely to specify systems. Hence, the need to write clear and accurate use case descriptions has a significant impact for many practitioners. However, many have pointed to weaknesses in the support offered to those writing use cases, and a number of authors advocate the use of rules in the composition and structuring of use case descriptions. These rules constrain the user, by only allowing certain grammatical constructions, typically guiding the structure or the style of the description For example, the CREWS research project pioneered Use Case Authoring Guidelines, suggesting that the adoption of such guidelines improved resulting use case descriptions. Replication of CREWS studies appeared to confirm the view that use case descriptions were improved through the application of guideline sets, but also noted that learning such rules presented a significant overhead. Hence, a leaner set of guidelines (the CP rules) was developed.This paper describes empirical work to assess the utility of these two sets of writing guidelines (CREWS and CP). In particular, descriptions are assessed against a set of established criteria-a use case quality description checklist, which the authors described in a previous paper.Our findings suggest that the leaner set of guidelines performs at least as well in terms of their ability to produce clear and accurate (comprehensible) descriptions. Hence, that a tractable set of rules may prove applicable to the industrial context, which could lead to effective validation of use cases.

Use cases have, for some years, been a popular approach to specification, as part of the Unified Modelling Language (UML). However, a number of authors have pointed to weaknesses with the approach, particularly in terms of the support offered to the writer of the use case description. This paper describes a Use Case Description Quality Checklist that acts as a check on the quality of the written description. The checklist is derived from theories of text comprehension, taken from the Discourse Processing community. The checklist approach has a number of benefits. First, the approach can be used to derive, or examine further, use case guidelines. That is, by considering whether such guidelines are likely to result in desirable qualities within the resulting description, one is able to make an informed judgement about the utility of those guidelines. Second, one can test for the desirable quality features in existing descriptions, thus enabling empirical validation. Third, as a minimum, the quality features can themselves be used as a checklist for the examination, and revision, of use case descriptions. To demonstrate applicability, the paper reports upon the use, and success, of the approach on an industrial case study.

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