DSDecode: A web tool for rapid decoding of superimposed sequencing chromatograms

Update: An updated version, DSDecodeM, is available at skl.scau.edu.cn. DSDecodeM allows uploading mutilple sequencing files at the same time, and decode more quickly than old version.

Sequence-specific nuclease-based genome targeting systems, i.e., TALENs and CRISPR/Cas9, often cause uniform biallelic and heterozygous mutations in diploid organisms. Direct sequencing of PCR products containing such mutations results in superimposed sequencing chromatograms. The Degenerate Sequence Decode (DSDecode) program serves to decode automatically sequencing chromatograms with biallelic, heterozygous, and homozygous mutations into allelic sequences.

For testing the program, two sequencing ab1 files and the corresponding references are provided. Click download to obtain the test files.

Upload a reference sequence

Please enter an intact reference sequence

It must completely cover the sequencing range of the ab1 file


The length of reference sequence should not be more than 5,000 bp

The program can search the two strands of the reference, so, it not necessary to convert the complement of the reference sequence.

Upload a chromatogram file
Enter a chromatogram (*.ab1) file

Set optional parameters

Target sequence of cleavage site (10-20 nt)


* It's an optional input parameter. But for low quality sequencing file, entering the target sequence would be helpful.

Length of anchor sequence (10-20 nt)

Length of degenerate sequence (10-50 nt)

Liu W., Xie X., Ma X., Li J., Chen J., and Liu Y.-G. 2015. DSDecode: A Web-based Tool for Decoding of Sequencing Chromatograms for Genotyping of Targeted Mutations. Mol. Plant (DOI: http://dx.doi.org/10.1016/j.molp.2015.05.009)
Ma X., Chen L., Zhu Q., Chen Y., and Liu Y.-G. 2015. Rapid Decoding of Sequence-Specific Nuclease-Induced Heterozygous and Biallelic Mutations by Direct Sequencing of PCR Products. Mol. Plant (DOI: http://dx.doi.org/10.1016/j.molp.2015.02.012)

Contact us

Copyright © The Genetic Engineering Laboratory of South China Agricultural University