Year 2020, Volume 3 , Issue 1, Pages 1 - 6 2020-03-20

Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors

Alper YILMAZ [1]


With the advent of natural language processing (NLP) techniques empowered with deep learning approaches, more detailed relationships between words have been unraveled. Word2Vec is quite robust in discovering contextual and semantic relationships. Genome being a long text, is subject to similar studies to unravel yet to be discovered relationships between DNA k-mers. Dna2vec applies Word2Vec approach to whole genome so that DNA k-mers are represented as vectors. The cosine similarity queries on DNA vectors reveal unusual relationships between DNA k-mers. In this study, we examined DNA sequence based prediction of mutation susceptibility. Initially,we generated word vectors for human and mouse genome via dna2vec. On the other hand, we retrieved coordinates of common and all mutations from dbSNP. For each coordinate, we extracted 8 nucleotide k-mers intersecting mutations and results are aggregated. such a way that number of mutations for each 8-mer has been tabulated. These results are incorporated with dna2vec cosine similarity data. Our results showed that for a given k-mer, k-mers with highest cosine similarity coincide with highest mutation count k-mer. In other words, the neighbor with the highest cosine similarity for a k-mer was also seen to be the neighbor overlapping the mutation count. As a result of our studies, human and mouse, dna2vec vs. mutation overlap is 80% and 70%, respectively. In conclusion, dna2vec and other word embedding approaches can be used to reveal mutation or variation characteristics of genomes without sequencing or experimental data, solely using the genome sequence itself. This might pave the way for understanding the underlying mechanism or dynamics of mutations in genomes.
mutation, word2vec, k-mer, dna2vec, cosine similarity
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Primary Language en
Subjects Computer Science, Artifical Intelligence
Published Date January 2020
Journal Section Research Articles
Authors

Orcid: 0000-0002-8827-4887
Author: Alper YILMAZ (Primary Author)
Institution: Yildiz Technical University
Country: Turkey


Dates

Application Date : January 14, 2020
Acceptance Date : February 7, 2020
Publication Date : March 20, 2020

Bibtex @research article { jista674910, journal = {Journal of Intelligent Systems: Theory and Applications}, issn = {}, eissn = {2651-3927}, address = {Sakarya Üniversitesi, Mühendislik Fakültesi, Endüstri Mühendisliği Bölümü, M5 Binası, Serdivan Sakarya.}, publisher = {Harun TAŞKIN}, year = {2020}, volume = {3}, pages = {1 - 6}, doi = {10.38016/jista.674910}, title = {Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors}, key = {cite}, author = {Yılmaz, Alper} }
APA Yılmaz, A . (2020). Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors . Journal of Intelligent Systems: Theory and Applications , 3 (1) , 1-6 . DOI: 10.38016/jista.674910
MLA Yılmaz, A . "Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors" . Journal of Intelligent Systems: Theory and Applications 3 (2020 ): 1-6 <https://dergipark.org.tr/en/pub/jista/issue/52473/674910>
Chicago Yılmaz, A . "Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors". Journal of Intelligent Systems: Theory and Applications 3 (2020 ): 1-6
RIS TY - JOUR T1 - Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors AU - Alper Yılmaz Y1 - 2020 PY - 2020 N1 - doi: 10.38016/jista.674910 DO - 10.38016/jista.674910 T2 - Journal of Intelligent Systems: Theory and Applications JF - Journal JO - JOR SP - 1 EP - 6 VL - 3 IS - 1 SN - -2651-3927 M3 - doi: 10.38016/jista.674910 UR - https://doi.org/10.38016/jista.674910 Y2 - 2020 ER -
EndNote %0 Zeki Sistemler Teori ve Uygulamaları Dergisi Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors %A Alper Yılmaz %T Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors %D 2020 %J Journal of Intelligent Systems: Theory and Applications %P -2651-3927 %V 3 %N 1 %R doi: 10.38016/jista.674910 %U 10.38016/jista.674910
ISNAD Yılmaz, Alper . "Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors". Journal of Intelligent Systems: Theory and Applications 3 / 1 (March 2020): 1-6 . https://doi.org/10.38016/jista.674910
AMA Yılmaz A . Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors. jista. 2020; 3(1): 1-6.
Vancouver Yılmaz A . Assessment of Mutation Susceptibility in DNA Sequences with Word Vectors. Journal of Intelligent Systems: Theory and Applications. 2020; 3(1): 1-6.