Improved assay-dependent searching of nucleic acid sequence databases.
Nucleic Acids Res
; 36(12): e74, 2008 Jul.
Article
em En
| MEDLINE
| ID: mdl-18515842
ABSTRACT
Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMantrade mark probe (i.e. in silico or 'virtual' PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Reação em Cadeia da Polimerase
/
Alinhamento de Sequência
/
Análise de Sequência de DNA
/
Bases de Dados de Ácidos Nucleicos
Tipo de estudo:
Evaluation_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2008
Tipo de documento:
Article
País de afiliação:
Estados Unidos