Reference - Detail
| RRC ID | 11900 |
|---|---|
| Author | Ishii S, Kadota K, Senoo K. |
| Title | Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data. |
| Journal | J Microbiol Methods |
| Abstract |
DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies. |
| Volume | 78(3) |
| Pages | 344-50 |
| Published | 2009-9-1 |
| DOI | 10.1016/j.mimet.2009.07.005 |
| PII | S0167-7012(09)00219-X |
| PMID | 19616587 |
| MeSH | Algorithms Cluster Analysis* DNA Fingerprinting / methods* Software |
| IF | 1.707 |
| Times Cited | 18 |
| WOS Category | BIOCHEMICAL RESEARCH METHODS MICROBIOLOGY |
| Altmetric score |
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| Total number of mentions | 0 |
| Resource | |
| General Microbes | JCM 1224 JCM 12893 JCM 13311 JCM 21032 JCM 21315 |