Molecular Biology
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 (72)
DNA-FAT can be downloaded here: dnafat (62)
Progamme idea by Marc Stegger (SSI), written by sharpe.
DNA Extractor – Utility for Invitrogens Vector NTI
by sharpe on Mar.25, 2009, under Molecular Biology, Utilities
DNA Extractor is an automated utility for extracting specifically formatted DNA sequences from data files such as those available at the National Center for Biotechnology Information. This can be done for both genomes and plasmids alike, as long as they keep the specific format. Genome and plasmid locations are read from genename files having the format specified in this file and actual DNA sequences are read from genedata files (specified in the XML configuration file).
By adding the desired details concerning which files to search, to the XML configuration file, the locally stored data files are searched for the gene locations (i.e. nt position 336..2798) of interest and all valid gene sequences are extracted from the specified file types (specified in the genedata element in the configuration file) and written to the output file (specified in the output element in the configuration file).
This format is specifically designed as input data for the Vector NTI programme suite for further analysis.
It can be download here dna-extractor (33). This is a beta release so use at your own risk.
