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- Title
Hepatitis C virus whole genome position weight matrix and robust primer design.
- Authors
Ping Qiu; Xiao-Yan Cai; Luquan Wang; Greene, Jonathan R.; Malcolm, Bruce
- Abstract
Background: The high degree of sequence heterogeneity found in Hepatitis C virus (HCV) isolates, makes robust nucleic acid-based assays difficult to generate. Polymerase chain reaction based techniques, require efficient and specific sequence recognition. Generation of robust primers capable of recognizing a wide range of isolates is a difficult task. Results: A position weight matrix (PWM) and a consensus sequence were built for each region of HCV and subsequently assembled into a whole genome consensus sequence and PWM. For each of the 10 regions, the number of occurrences of each base at a given position was compiled. These counts were converted to frequencies that were used to calculate log odds scores. Using over 100 complete and 14,000 partial HCV genomes from GenBank, a consensus HCV genome sequence was generated along with a PWM reflecting heterogeneity at each position. The PWM was used to identify the most conserved regions for primer design. Conclusions: This approach allows rapid identification of conserved regions for robust primer design and is broadly applicable to sets of genomes with all levels of genetic heterogeneity.
- Subjects
HEPATITIS C virus; GENOMES; POLYMERASE chain reaction; NUCLEOTIDE sequence; HETEROGENEITY
- Publication
BMC Microbiology, 2002, Vol 2, p29
- ISSN
1471-2180
- Publication type
Article
- DOI
10.1186/1471-2180-2-29