Simrank: A Fast Tool for Finding Similar Sequences
Author Information
Author(s): DeSantis Todd Z, Keller Keith, Karaoz Ulas, Alekseyenko Alexander V, Singh Navjeet N, Brodie Eoin L, Pei Zhiheng, Andersen Gary L, Larsen Niels
Primary Institution: Lawrence Berkeley National Laboratory
Hypothesis
A rapid, general-purpose, open-source k-mer tool is needed for molecular ecologists.
Conclusion
Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.
Supporting Evidence
- Simrank is 10X to 928X faster than other tools depending on the dataset.
- It can handle up to 2 billion sequences.
- Simrank allows for user-defined search depths and k-mer sizes.
- It is open-source and can be integrated into various computational pipelines.
Takeaway
Simrank is a computer program that helps scientists quickly find similar DNA, RNA, or protein sequences, making their research faster and easier.
Methodology
Simrank is implemented as an object-oriented PERL module with a C function for efficiency, allowing users to compare sequences without alignment.
Limitations
Simrank may not be suitable for searching randomly shuffled DNA or for matching proteins with highly variable content.
Digital Object Identifier (DOI)
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