Genomic PCR simulation with hardware-accelerated approximate sequence matching

被引：0
|
作者：
Lexa, Matej [1 ]
Martinek, Tomas [2 ]
Beck, Patrik [2 ]
Fucik, Otto [2 ]
Valle, Giorgio [3 ]
Zara, Ivano [3 ]
机构：
[1] Masaryk Univ, Fac Informat, Botan 68, Brno 60200, Czech Republic
[2] Brno Univ Technol, Fac Informat Technol, Brno 61266, Czech Republic
[3] Univ Padua, CRIBI Biotechol Ctr, I-35133 Padua, Italy
来源：
21ST EUROPEAN CONFERENCE ON MODELLING AND SIMULATION ECMS 2007: SIMULATIONS IN UNITED EUROPE | 2007年
关键词：
PCR; simulation; PRIMEX; approximate matching; similarity search; oligonucleotide melting; hardware; acceleration; FPGA;
D O I：
暂无
中图分类号：
TP18 [人工智能理论];
学科分类号：
081104 ; 0812 ; 0835 ; 1405 ;
摘要：
We report the latest details on improvements made or planned for the VPCR simulation software currently accessible on the Internet (installed on servers in Padova and Brno). We describe the inner workings of the dynamic amplification simulation model, concentrating mostly on the time- and sensitivity-critical step of sequence matching. Replacement of BLAST by the more sensitive and faster PRIMEX similarity search program resulted in a marked improvement of PCR product predictions. Further speed improvements were acheived using hardware acceleration of approximate sequence matching. We report our theorethical computation time estimates and results of the first tests using the Arabidopis and human genome sequences as PCR templates.
引用
收藏
页码：333 / +
页数：2
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