Multiple sequence alignment (MSA) is one of the most useful tools in bioinformatics. MSA plays a key role in protein/RNA structure prediction, phylogenetic analysis or pattern identification among other important bioinformatic applications. However, the growth of sequencing data imposes further difficulties to aligning it with traditional tools. For large-scale alignments with thousands of sequences or even whole genomes, it will be necessary to use and take advantage of high performance computing (HPC). This paper, focused on a consistency-based MSA tool called T-Coffee, presents several innovative solutions; the Balanced Guide Tree, the Optimized Library Method and the Multiple Tree Alignment. The results obtained by the methods presented have demonstrated that it is possible to improve efficiency, scalability and accuracy.
In order to ensure a more widespread implementation of video-ondemand (VoD) services, it is essential that the design of cost-effective largescale VoD (LVoD) architectures be able to support hundreds of thousands of concurrent users. The main keys for the designing of such architectures are high streaming capacity, low costs, scalability, fault tolerance, load balance, low complexity and resource sharing among user requests. To achieve these objectives, we propose a distributed architecture, called double P-Tree, which is based on a tree topology of independent local networks with proxies. The proxy functionality has been modified in such a way that it works at the same time as cache for the most-watched videos, and as a distributed mirror for the remaining videos. In this way, we manage to distribute main server functionality (as a repository of all system videos, server of proxy-misses and system manager) among all local proxies. The evaluation of this new architecture, through an analytical model, shows that double P-Tree architecture is a good approach for the building of scalable and fault-tolerant LVoD systems. Experimental results show that this architecture achieves a good tradeoff between effective bandwidth and storage requirements.
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