Literature DB >> 21068001

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.

Qing Yu1, Elizabeth M Ryan, Todd M Allen, Bruce W Birren, Matthew R Henn, Niall J Lennon.   

Abstract

SUMMARY: PriSM is a set of algorithms designed to select and match degenerate primer pairs for the amplification of viral genomes. The design of panels of hundreds of primer pairs takes just hours using this program, compared with days using a manual approach. PriSM allows for rapid in silico optimization of primers for downstream applications such as sequencing. As a validation, PriSM was used to create an amplification primer panel for human immunodeficiency virus (HIV) Clade B. AVAILABILITY: The program is freely available for use at: www.broadinstitute.org/perl/seq/specialprojects/primerDesign.cgi.

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Year:  2010        PMID： 21068001      PMCID： PMC3018813          DOI： 10.1093/bioinformatics/btq624

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

1.  Primer3 on the WWW for general users and for biologist programmers.

Authors:  S Rozen; H Skaletsky
Journal:  Methods Mol Biol       Date:  2000

2.  Amplicon: software for designing PCR primers on aligned DNA sequences.

Authors:  Simon N Jarman
Journal:  Bioinformatics       Date:  2004-02-12       Impact factor: 6.937

3.  Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection.

Authors:  Zabrina L Brumme; Chanson J Brumme; Jonathan Carlson; Hendrik Streeck; Mina John; Quentin Eichbaum; Brian L Block; Brett Baker; Carl Kadie; Martin Markowitz; Heiko Jessen; Anthony D Kelleher; Eric Rosenberg; John Kaldor; Yuko Yuki; Mary Carrington; Todd M Allen; Simon Mallal; Marcus Altfeld; David Heckerman; Bruce D Walker
Journal:  J Virol       Date:  2008-07-09       Impact factor: 5.103

4.  Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution.

Authors:  M Martell; J I Esteban; J Quer; J Genescà; A Weiner; R Esteban; J Guardia; J Gómez
Journal:  J Virol       Date:  1992-05       Impact factor: 5.103

5.  PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.

Authors:  Jakob Fredslund; Leif Schauser; Lene H Madsen; Niels Sandal; Jens Stougaard
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

6.  PrimerZ: streamlined primer design for promoters, exons and human SNPs.

Authors:  Ming-Fang Tsai; Yi-Jung Lin; Yu-Chang Cheng; Kuo-Hsi Lee; Cheng-Chih Huang; Yuan-Tsong Chen; Adam Yao
Journal:  Nucleic Acids Res       Date:  2007-05-30       Impact factor: 16.971
  6 in total
  6 in total

1.  Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Authors:  Poornima Parameswaran; Patrick Charlebois; Yolanda Tellez; Andrea Nunez; Elizabeth M Ryan; Christine M Malboeuf; Joshua Z Levin; Niall J Lennon; Angel Balmaseda; Eva Harris; Matthew R Henn
Journal:  J Virol       Date:  2012-05-30       Impact factor: 5.103

2.  Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

Authors:  Astrid Gall; Bridget Ferns; Clare Morris; Simon Watson; Matthew Cotten; Mark Robinson; Neil Berry; Deenan Pillay; Paul Kellam
Journal:  J Clin Microbiol       Date:  2012-09-19       Impact factor: 5.948

3.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Authors:  Joshua Quick; Nathan D Grubaugh; Steven T Pullan; Ingra M Claro; Andrew D Smith; Karthik Gangavarapu; Glenn Oliveira; Refugio Robles-Sikisaka; Thomas F Rogers; Nathan A Beutler; Dennis R Burton; Lia Laura Lewis-Ximenez; Jaqueline Goes de Jesus; Marta Giovanetti; Sarah C Hill; Allison Black; Trevor Bedford; Miles W Carroll; Marcio Nunes; Luiz Carlos Alcantara; Ester C Sabino; Sally A Baylis; Nuno R Faria; Matthew Loose; Jared T Simpson; Oliver G Pybus; Kristian G Andersen; Nicholas J Loman
Journal:  Nat Protoc       Date:  2017-05-24       Impact factor: 13.491

Review 4.  Unraveling the web of viroinformatics: computational tools and databases in virus research.

Authors:  Deepak Sharma; Pragya Priyadarshini; Sudhanshu Vrati
Journal:  J Virol       Date:  2014-11-26       Impact factor: 5.103

5.  Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues.

Authors:  Jin Sun No; Won-Keun Kim; Seungchan Cho; Seung-Ho Lee; Jeong-Ah Kim; Daesang Lee; Dong Hyun Song; Se Hun Gu; Seong Tae Jeong; Michael R Wiley; Gustavo Palacios; Jin-Won Song
Journal:  Sci Rep       Date:  2019-11-12       Impact factor: 4.379

6.  A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.

Authors:  Elizabeth M Batty; T H Nicholas Wong; Amy Trebes; Karène Argoud; Moustafa Attar; David Buck; Camilla L C Ip; Tanya Golubchik; Madeleine Cule; Rory Bowden; Charis Manganis; Paul Klenerman; Eleanor Barnes; A Sarah Walker; David H Wyllie; Daniel J Wilson; Kate E Dingle; Tim E A Peto; Derrick W Crook; Paolo Piazza
Journal:  PLoS One       Date:  2013-06-10       Impact factor: 3.240
  6 in total

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