Tag: Staphylococcus Aureus
DNA FAT – DNA Frequency Analysis Tool
by sharpe on May.20, 2010, under Molecular Biology, Utilities
DNA-FAT performs a very rapid indexation of the uniqueness and repetitative buildup of fasta format DNA sequences using user assigned window sizes.
The two output files contain the following:
- The number of unique sequences with the preset window size and the number of sequences present, any number of multiple times.
- Output of the actual sequences themselves and their number of repetitions in the input DNA sequence.
One of the possible uses of the program is to evaluate the required DNA sequencing length of the new next-generation sequencing technologies such as Illumina’s Genome Analyzer and ABI’s SOLiD platform, to predict a high number of unique matches when performing techniques such as RNAseq.
Here is a screen-dump of dnafat in action:
Below is an example of an output file using the genome sequences Staphylococcus Aureus USA300 (NC_007793):
- Extracted sequences report: dnafat sequence report (76)
- Analysis report: dnafat results report (71)
DNA-FAT can be downloaded here: dnafat (61)
Progamme idea by Marc Stegger (SSI), written by sharpe.
