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

Bioinformatics

Volumn 27, Issue 2, 2011, Pages 266-267

  Yu, Qing ^a   Ryan, Elizabeth M ^a   Allen, Todd M ^b   Birren, Bruce W ^a   Henn, Matthew R ^a   Lennon, Niall J ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS;

PRIMER DNA;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VALIDATION STUDY; VIRUS GENOME;

ALGORITHMS; DNA PRIMERS; GENOME, VIRAL; HIV; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 78651460018     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq624     Document Type: Article

References (6)

1. Brumme,Z.L. et al. (2008) 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. J. Virol., 82, 9216-9227.
2. Fredslund,J. et al. (2005) PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res., 33, 20.
3. Jarman,S.N. (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644-1645.
4. Martell,M. et al. (1992) Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J. Virol., 66, 3225-3229.
5. Rozen,S. and Skaletsky,H.J. (2000) Primer3 on the WWW for general users and for biologist programmers. In Krawetz,S. and Misener,S. (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp. 365-386.
6. Tsai,M. et al. (2007) PrimerZ: streamlined primer design for promoters, exons and human SNPs. Nucleic Acids Res., 35, W65.