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High level synthesis of Smith-Waterman dataflow implementations

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Field-programmable gate array

A field-programmable gate array (FPGA) is an integrated circuit designed to be configured after manufacturing. The FPGA configuration is generally specified using a hardware description language (HDL), similar to that used for an application-specific integrated circuit (ASIC). Circuit diagrams were previously used to specify the configuration, but this is increasingly rare due to the advent of electronic design automation tools. FPGAs contain an array of programmable logic blocks, and a hierarchy of reconfigurable interconnects allowing blocks to be wired together.

High-level synthesis

High-level synthesis (HLS), sometimes referred to as C synthesis, electronic system-level (ESL) synthesis, algorithmic synthesis, or behavioral synthesis, is an automated design process that takes an abstract behavioral specification of a digital system and finds a register-transfer level structure that realizes the given behavior. Synthesis begins with a high-level specification of the problem, where behavior is generally decoupled from low-level circuit mechanics such as clock-level timing.

Logic synthesis

In computer engineering, logic synthesis is a process by which an abstract specification of desired circuit behavior, typically at register transfer level (RTL), is turned into a design implementation in terms of logic gates, typically by a computer program called a synthesis tool. Common examples of this process include synthesis of designs specified in hardware description languages, including VHDL and Verilog. Some synthesis tools generate bitstreams for programmable logic devices such as PALs or FPGAs, while others target the creation of ASICs.

Sequence alignment

In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.

Xilinx

Xilinx, Inc. (ˈzaɪlɪŋks ) was an American technology and semiconductor company that primarily supplied programmable logic devices. The company is known for inventing the first commercially viable field-programmable gate array (FPGA) and creating the first fabless manufacturing model. Xilinx was co-founded by Ross Freeman, Bernard Vonderschmitt, and James V Barnett II in the year 1984 and the company went public on the NASDAQ in the year 1990.

C to HDL

C to HDL tools convert C language or C-like computer code into a hardware description language (HDL) such as VHDL or Verilog. The converted code can then be synthesized and translated into a hardware device such as a field-programmable gate array. Compared to software, equivalent designs in hardware consume less power (yielding higher performance per watt) and execute faster with lower latency, more parallelism and higher throughput.

Non-functional requirement

In systems engineering and requirements engineering, a non-functional requirement (NFR) is a requirement that specifies criteria that can be used to judge the operation of a system, rather than specific behaviours. They are contrasted with functional requirements that define specific behavior or functions. The plan for implementing functional requirements is detailed in the system design. The plan for implementing non-functional requirements is detailed in the system architecture, because they are usually architecturally significant requirements.

Hardware description language

In computer engineering, a hardware description language (HDL) is a specialized computer language used to describe the structure and behavior of electronic circuits, and most commonly, digital logic circuits. A hardware description language enables a precise, formal description of an electronic circuit that allows for the automated analysis and simulation of an electronic circuit.

Business requirements

Business requirements, also known as stakeholder requirements specifications (StRS), describe the characteristics of a proposed system from the viewpoint of the system's end user like a CONOPS. Products, systems, software, and processes are ways of how to deliver, satisfy, or meet business requirements. Consequently, business requirements are often discussed in the context of developing or procuring software or other systems. Three main reasons for such discussions: A common practice is to refer to objectives, or expected benefits, as 'business requirements.

Multiple sequence alignment

Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.