Genome-wide primer scan (GPS): a python package for a flexible, reliable and large-scale primer design toolkit  

作　　者：Wencong HE Yan ZHUO Chen WANG Yemei HUANG Xuelei ZANG Chen YANG Hengyu DENG Yangyu ZHOU Jing LIU Ping ZHANG Xinying XUE Liye ZHANG 

机构地区：[1]School of Life Science and Technology,ShanghaiTech University,Shanghai 201210,China [2]Shanghai Institute for Advanced Immunochemical Studies,ShanghaiTech University,Shanghai 201210,China [3]Department of Respiratory and Critical Care,Emergency and Critical Care Medical Center,Beijing Shijitan Hospital,Capital Medical University,Beijing 100038,China [4]Medical School of Chinese PLA,Beijing 100853,China [5]Department of Respiratory and Critical Care,Shandong Second Medical University,Weifang 261053,China [6]Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology,College of Life Sciences,Beijing Normal University,Beijing 100875,China

出　　处：《Frontiers of Computer Science》2025年第2期127-128,共2页计算机科学前沿(英文版)

基　　金：supported by the National Key R&D Program of China(SQ2021YFC2300067).

摘　　要：1 Introduction Microbial infections represent significant global health challenges with far-reaching implications.In contemporary medical practice,quantitative polymerase chain reaction(qPCR)stands as an important technique for pathogen detection,and the success of qPCR-based diagnosis fundamentally depends on the precision of the qPCR primers employed[1].However,to our knowledge,no easy-to-use qPCR primer design tool with flexible,customized options is available.In most clinical contexts,detecting the presence of a pathogen within a given clinical sample is the primary objective.Therefore,well-designed primers should achieve dual objectives:high sensitivity and specificity for detecting target pathogens,while avoiding false positives,even when testing evolutionarily closely related pathogens.Currently,a constellation of software and program packages towards qPCR primer design is available(for example,ssPrimer).However,these tools typically operate on a single gene or region,necessitating user-driven selection of the region or gene[2,3].In this context,we introduce the first one-step solution,to our knowledge,for scanning entire genomes to identify the best candidate primer sets.In addition,our framework allows users to efficiently search against a large number of genomes(over 1,800 genomes in our test case)to identify specific primers.

关 键 词：PYTHON false typically 

分 类 号：TP3[自动化与计算机技术—计算机科学与技术]