OPTIMAL AREA AND PERFORMANCE MAPPING OF K-LUT BASED FPGAS

FPGA circuits are increasingly used in many fields: for rapid prototyping of new products (including fast ASIC implementation), for logic emulation, for producing a small number of a device, or if a device should be reconfigurable in use (reconfigurable computing). Determining if an arbitrary, given wide, function can be implemented by a programmable logic block, unfortunately, it is generally, a very difficult problem. This problem is called the Boolean matching problem. This paper introduces a new implemented algorithm able to map, both for area and performance, combinational networks using k-LUT based FPGAs.k-LUT based FPGAs, combinational circuits, performance-driven mapping.

OPTIMIZING LARGE COMBINATIONAL NETWORKS FOR K-LUT BASED FPGA MAPPING

Optimizing by partitioning is a central problem in VLSI design automation, addressing circuit’s manufacturability. Circuit partitioning has multiple applications in VLSI design. One of the most common is that of dividing combinational circuits (usually large ones) that will not fit on a single package among a number of packages. Partitioning is of practical importance for k-LUT based FPGA circuit implementation. In this work is presented multilevel a multi-resource partitioning algorithm for partitioning large combinational circuits in order to efficiently use existing and commercially available FPGAs packagestwo-way partitioning, multi-way partitioning, recursive partitioning, flat partitioning, critical path, cutting cones, bottom-up clusters, top-down min-cut

Identification of mammalian orthologs using local synteny

<p>Abstract</p> <p>Background</p> <p>Accurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication, and high rates of retrotransposition all combine to make inference of orthology between genes difficult. Many methods have been developed to identify orthologous genes, mostly based upon analysis of the inferred protein sequence of the genes. More recently, methods have been proposed that use genomic context in addition to protein sequence to improve orthology assignment in vertebrates. Such methods have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates. However, to our knowledge, no explicit comparison of synteny and sequence based definitions of orthology has been reported in vertebrates, or, more specifically, in mammals.</p> <p>Results</p> <p>We test a simple method for the measurement and utilization of gene order (local synteny) in the identification of mammalian orthologs by investigating the agreement between coding sequence based orthology (Inparanoid) and local synteny based orthology. In the 5 mammalian genomes studied, 93% of the sampled inter-species pairs were found to be concordant between the two orthology methods, illustrating that local synteny is a robust substitute to coding sequence for identifying orthologs. However, 7% of pairs were found to be discordant between local synteny and Inparanoid. These cases of discordance result from evolutionary events including retrotransposition and genome rearrangements.</p> <p>Conclusions</p> <p>By analyzing cases of discordance between local synteny and Inparanoid we show that local synteny can distinguish between true orthologs and recent retrogenes, can resolve ambiguous many-to-many orthology relationships into one-to-one ortholog pairs, and might be used to identify cases of non-orthologous gene displacement by retroduplicated paralogs.</p