Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.
Omar Jabado,Gustavo Palacios,Vishal Kapoor,Jeffrey Hui,Neil Renwick,Junhui Zhai,Thomas Briese,W. Ian Lipkin +7 more
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TLDR
A method for designing degenerate primers based on tree building followed by application of a set covering algorithm is presented and its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens is demonstrated.Abstract:
Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.read more
Citations
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A new arenavirus in a cluster of fatal transplant-associated diseases.
Gustavo Palacios,Julian Druce,Lei Du,Thomas Tran,Chris Birch,Thomas Briese,Sean Conlan,Phuong-Lan Quan,Jeffrey Hui,John C. Marshall,Jan Fredrik Simons,Michael Egholm,Christopher D. Paddock,Wun-Ju Shieh,Cynthia S. Goldsmith,Sherif R. Zaki,Mike Catton,W. Ian Lipkin +17 more
TL;DR: The use of high-throughput sequencing during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation, related to lymphocytic choriomeningitis viruses.
Journal ArticleDOI
Bioinformatic challenges for DNA metabarcoding of plants and animals
TL;DR: The use of DNA metabarcoding in the assessment of biodiversity in plant and animal communities is under-explored as mentioned in this paper, and several unique features of DNA barcoding justify the development of specific data analysis methodologies.
Journal ArticleDOI
MPprimer: a program for reliable multiplex PCR primer design
Zhiyong Shen,Wubin Qu,Wen Wang,Yiming Lu,Yonghong Wu,Zhifeng Li,Xingyi Hang,Xiaolei Wang,Dongsheng Zhao,Chenggang Zhang +9 more
TL;DR: MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays and provides a virtual electrophotogram to help users choose the best PSC.
Journal ArticleDOI
Metagenomics for the discovery of novel human viruses.
Patrick Tang,Charles Y. Chiu +1 more
TL;DR: Metagenomics-based tools, such as microarrays and high-throughput sequencing, have the potential to detect the full spectrum of viruses, including those present in low numbers.
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Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
TL;DR: This study demonstrates a trade-off between the evolution of a non-visual sensory system and eye regression during the adaptive evolution of Astyanax to the cave environment.
References
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Book
Computers and Intractability: A Guide to the Theory of NP-Completeness
TL;DR: The second edition of a quarterly column as discussed by the authors provides a continuing update to the list of problems (NP-complete and harder) presented by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NP-Completeness,” W. H. Freeman & Co., San Francisco, 1979.
Book ChapterDOI
Primer3 on the WWW for general users and for biologist programmers.
Steve Rozen,Helen Skaletsky +1 more
TL;DR: This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs.
Journal ArticleDOI
Multiple sequence alignment with the Clustal series of programs
Ramu Chenna,Hideaki Sugawara,Tadashi Koike,Rodrigo Lopez,Toby J. Gibson,Desmond G. Higgins,Julie D. Thompson +6 more
TL;DR: The Clustal series of programs, widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees, are extended.
Journal ArticleDOI
Open source clustering software
TL;DR: This work has implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs.
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