Conclusion and Future Direction
We have developed a GUI-based JSequitur, based on string compression algorithms, to examine grammatical traits of biological sequences. On top of compression capacity, a string compression algorithm is appealing for studying biological sequences, because it can give insights into the structure of these sequences. Precisely constructed models for linguistic structure can play a vital role in the process of discovery itself.
We also applied JSequitur to analyze 104 cancer genes for testing purposes only. Even though there are some interesting results in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate, our test samples were too small to conclude anything. Thus, our result should be regarded as preliminary for future research. We should consider various factors other than grammatical structures and compression rates.
As our main purpose of developing the tool was to examine any grammatical traits of biological sequences, the graphical user interface was important for a semiautomatic screening process. However, we still need to implement various features to compare gene structures to summarize statistics in regards to grammatical structures and to combine evolutionary trees. Hopefully, these features will be implemented in the next version of JSequitur. We also hope to enhance the algorithm more elaborately to handle reversal, translocation, and shuffling.