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ShortCAKE - Shortest Sequence to Cover All K-mers
ShortCAKE (short for Shortest sequence to Cover All K-mErs) is a software for
generating a shortest sequence that for each DNA k-mer includes the k-mer or its reverse complement.
In other words, it generates a shortest possible double-stranded sequence covering all k-mers.
ShortCAKE can also generate the longest k-unique DNA sequence.
For each k-mer the sequence may include the k-mer or its reverse complement, but not both.
Input and Output
ShortCAKE takes as input four parameters:
1. a/d - shortest sequence that cover all k-mers / longest k-unique sequence.
2. k - the order of the sequence.
3. The output file name.
4. 0/1 - a suboptimal linear time algorithm / an optimal polynomial time algorithm.
It outputs the sequence as a textual file.
ShortCAKE was developed by Yaron Orenstein in Ron Shamir's Computational Genomics group at Tel Aviv University.
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Get the software
Java executable distribution and example files
This distribution is our officially supported executable for
ShortCAKE. This binary is completely self-contained and should
work out of the box without any issues.
The package includes a README file and example output files for optimal sequences for k=2,3,4,5,6,7,8,9,10.
The software is freely available under the GNU Lesser General Public License, version 3, or any later version at your choice.
ShortCAKE is a research software, still in the development stage. Hence, it is not presented as error-free, accurate, complete, useful, suitable for any specific application or free from any infringement of any rights. The Software is licensed AS IS, entirely at the user's own risk.
How to use it
java -jar ShortCAKE.jar <a/d> <k> <output_filename> <0/1>
Example runs:
java -jar ShortCAKE.jar a 8 sequence8.txt 0
java -jar ShortCAKE.jar d 7 sequence7.txt 1
java -jar ShortCAKE.jar d 10 sequence10.txt 1
Interpreting the output
The output file is a text file containing the sequence.
* Note that the sequence is cyclic. This means that the last k-1 k-mers are missing.
To correct this, attach the first k-1 characters to the end of the sequence.
Citing ShortCAKE
ShortCAKE can be cited as follows:
Design of Shortest Double-Stranded DNA Sequences Covering All K-mers with Applications to Protein Binding Microarrays and Synthetic Enhancers,
Yaron Orenstein, Ron Shamir.
Vol. 29 (13), Pages i71-i79, Bioinformatics (2013).
doi: 10.1093/bioinformatics/btt230
Optimal Design of k-Unique DNA Sequence
Yaron Orenstein, Ron Shamir.
In preparation
Get in touch
In case of any questions or suggestions please feel free to contact Yaron Orenstein.