Pyrosequencing Primer Design for Forensic Biology Applications

2021 ◽  
pp. 247-259
Author(s):  
Kelly M. Elkins
2001 ◽  
Vol 1 ◽  
pp. 605-608
Author(s):  
Walter Rowe

At the beginning of a new millennium it seems a good idea to stop for a moment and take stock of the current state of forensic science. As a field of scientific research and scientific application, forensic science is a little more than a century old. Forensic science may be said to have begun in 1887 with the simultaneous publication of A. Conan Doyle’s A Study in Scarlet and Hans Gross’s Handbuch für Untersuchungsrichter. Conan Doyle’s novel introduced to the world the character of Sherlock Holmes, whose literary career would popularize the use of physical evidence in criminal investigations. Gross’s manual for examining magistrates suggests ways in which the expertise of chemists, biologists, geologists, and other natural scientists could contribute to investigations. Gross’s book was translated into a number of languages and went through various updated editions during the course of the century. The intervening century saw the development and application of fingerprinting, firearm and tool mark identification, forensic chemistry, forensic biology, forensic toxicology, forensic odontology, forensic pathology, and forensic engineering. Increasingly, the judicial systems of the industrial nations of the world have come to rely upon the expertise of scientists in a variety of disciplines. In most advanced countries, virtually all criminal prosecutions now involve the presentation of scientific testimony. This has had the beneficial effect of diminishing the reliance of courts on eyewitness testimony and defendant confessions.


Author(s):  
Takeshi Toda ◽  
Shun Hanesaka ◽  
Kuniaki Shishido ◽  
Shin-ichi Fuji ◽  
Hiromitsu Furuya

AbstractPrimers specific for the hypothetical forma specialis of Fusarium oxysporum were designed to amplify DNA from this pathogenic fungus that infects plants including lilies. The F. oxysporum sequence between the transposal elements han and hop was used for primer design. Three primer pairs designed from this region were confirmed as specific for 24 isolates of F. oxysporum pathogenic to lilies, except for one pathogenic isolates as extraordinary. No amplification was observed from F. oxysporum non-pathogenic to lily, from 12 forma specialis, and 14 fungi and oomycetes concerned with Liliaceae plants. We propose that specific primers designed from this region will be useful to detect isolates of F. oxysporum that are pathogenic to lilies.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jeongmin Bae ◽  
Hajin Jeon ◽  
Min-Soo Kim

Abstract Background Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB. Due to the effectiveness of primers designed by MRPrimer in qPCR analysis, it has been widely used for developing many online design tools and building primer databases. However, the computational speed of MRPrimer is too slow to deal with the sizes of sequence DBs growing exponentially and thus must be improved. Results We develop a fast GPU-based pipeline for primer design (GPrimer) that takes the same input and returns the same output with MRPrimer. MRPrimer consists of a total of seven MapReduce steps, among which two steps are very time-consuming. GPrimer significantly improves the speed of those two steps by exploiting the computational power of GPUs. In particular, it designs data structures for coalesced memory access in GPU and workload balancing among GPU threads and copies the data structures between main memory and GPU memory in a streaming fashion. For human RefSeq DB, GPrimer achieves a speedup of 57 times for the entire steps and a speedup of 557 times for the most time-consuming step using a single machine of 4 GPUs, compared with MRPrimer running on a cluster of six machines. Conclusions We propose a GPU-based pipeline for primer design that takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB at once without an additional step using BLAST-like tools. The software is available at https://github.com/qhtjrmin/GPrimer.git.


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