csDMA

csDMA (cross-species DNA 6mA modification analyzer) is a software tool for analyzing 6mA modifications in DNA sequences across different species.

Key features of csDMA include:

1. Identification of 6mA sites in DNA sequences from various species

2. Characterization of sequence motifs associated with 6mA modifications

3. Comparative analysis of 6mA patterns across different species or samples

4. Visualization of 6mA distribution along DNA sequences

5. Integration with other genomic features and annotations

csDMA takes DNA sequences in FASTA format as input and outputs the predicted 6mA sites, motifs, and comparative analysis results. The tool utilizes machine learning algorithms trained on known 6mA sites to predict novel modifications in the input sequences.

Topic

Machine learning;Methylated DNA immunoprecipitation;Gene transcripts

Detail

  • Operation: -

  • Software interface: Command-line interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The Start-up foundation of Northwest A&F University, the National Natural Science Foundation of China, the Postdoctoral Research Foundation of China.

  • Input: FASTA

  • Output: -

  • Contact: Wei Dong dongw@nwafu.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • csDMA: an improved bioinformatics tool for identifying DNA 6 mA modifications via Chou's 5-step rule.
  • Liu Z, et al. csDMA: an improved bioinformatics tool for identifying DNA 6 mA modifications via Chou's 5-step rule. csDMA: an improved bioinformatics tool for identifying DNA 6 mA modifications via Chou's 5-step rule. 2019; 9:13109. doi: 10.1038/s41598-019-49430-4
  • https://doi.org/10.1038/S41598-019-49430-4
  • PMID: 31511570
  • PMC: PMC6739324

Download and documentation

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