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.
Bibliographical noteFunding Information:
This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) from Bio-oriented Technology Research Advancement Institution, Japan (to SI and KS). Additional financial support was provided by Special Coordination Funds for Promoting Science and Technology, and by a Grant-in-Aid for Scientific Research (No. 19700273 ) from Japan Society for the Promotion of Science (to KK) .
- Complete linkage clustering
- DNA fingerprinting
- Peak alignment
- R program