Shared probe design and existing microarray reanalysis using PICKY

<p>Abstract</p> <p>Background</p> <p>Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations.</p> <p>Results</p> <p><smcaps>PICKY</smcaps> 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. <smcaps>PICKY</smcaps> 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, <smcaps>PICKY</smcaps> does not sacrifice the quality of shared probes when choosing them. The latest <smcaps>PICKY</smcaps> 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making <smcaps>PICKY</smcaps> 2.1 more versatile to microarray users.</p> <p>Conclusions</p> <p>Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.</p

Understanding the Middle East peace process: a historical institutionalist approach

This article challenges the common assumption that the external actors involved in the Middle East Peace Process (MEPP) are driven either by neo-realist strategic competition or by the constraining power of domestic lobbies, or by a mixture of both. Such implicit assumptions are evident in the controversial argument of the power of the ‘Israel lobby’ as promoted by Stephen Walt and John Mearsheimer. This article argues that approaches based on such assumptions fail to explain adequately the policies adopted not only by the United States, but also by other key external actors who have been historically engaged in the MEPP — the Soviet Union and the European Union. A better explanatory framework is provided by treating the MEPP as an institution and by applying a historical institutionalist approach to the development of the MEPP, using such concepts as critical junctures, path dependence and positive feedback to analyse how the main external actors involved in the MEPP came to adopt their distinctive national approaches to the peace process. In particular, it is the responses of these actors to certain critical junctures, most notably but not exclusively to the period of the 1967 and 1973 Arab–Israeli wars, that has had a particularly strong influence on policy formulation. For the US case, the creative policymaking of Henry Kissinger during the period after the 1973 war, which was subsequently incorporated into the US conceptualization of the MEPP, provides powerful and generally unrecognized insights into the initial puzzle identified by Walt and Mearsheimer — the consistent and almost unconditional support given to Israel by the United States despite the strategic problems this creates for broader US Middle East policy