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Background: Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determination of protein domains and their boundaries. We provide and rigorously evaluate a novel set of domain families that is automatically generated from sequence data. Our domain family identification process, called EVEREST (EVolutionary Ensembles of REcurrent SegmenTs), begins by constructing a library of protein segments that emerge in an all vs. all pairwise sequence comparison. It then proceeds to cluster these segments into putative domain families. The selection of the best putative families is done using machine learning techniques. A statistical model is then created for each of the chosen families. This procedure is then iterated: the aforementioned statistical models are used to scan all protein sequences, to recreate a library of segments and to cluster them again.

This paper deals with the integration process in technological systems projects. The paper reviews the objectives of the integration process, planning and managing principles, as well as the pitfalls and difficulties associated with this process. The following integration approaches are described and analyzed: hardware-assisted versus software only, bottom-up versus top-down, and hierarchial versus functional approaches. Then, a case study that focuses on the third group-the hierarchial and functional approaches-is presented. Four projects that were conducted at the same firm have been examined. The case study attempts to determine whether there is a relation between these two integration approaches and project success. The findings of the case study show that-particularly when customer satisfaction is determined as a major goal-the hierarchial integration approach is preferable to the functional approach, with respect to project success.

The full C++ source code for SPRINT can be freely downloaded from http://www.protonet.cs.huji.ac.il/sprint.

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