• A
  • A
  • A
  • ABC
  • ABC
  • ABC
  • А
  • А
  • А
  • А
  • А
Regular version of the site

Student
Title
Supervisor
Faculty
Educational Programme
Final Grade
Year of Graduation
Alexander Shein
Transposon Recognition by Machine-Learning Methods
Big Data Systems
(Master’s programme)
9
2019
The role of 3’ UTR stem-loops secondary structures in retrotransposition was experimentally shown for mobile genetic elements of various species, where LINE and SINE retrotransposons share the same 3’ UTR sequences, containing a stem-loop. The properties of 3’-end stem-loops of human L1s, Alus, were investigated. They do not match in terms of sequences, but all have 3’ UTR stem-loops. Two types of machine-learning models have been built: a sequence-based and a structure-based in order to recognize 3’-end L1 and Alu, stem-loops with high accuracy. The sequence-based models consider only sequence statistics information and capture compositional bias in 3’-ends. The structure-based models take into account chemical, physical and geometrical characteristics of dinucleotides in a stem and position-specific nucleotide features of a loop and a bulge. The most significant parameters include shift, rise, tilt, and hydrophilicity. Obtained results point to the existence of some structural constrains for 3’ UTR stem-loops of L1 and Alu, which are probably required for transposition.

Student Theses at HSE must be completed in accordance with the University Rules and regulations specified by each educational programme.

Summaries of all theses must be published and made freely available on the HSE website.

The full text of a thesis can be published in open access on the HSE website only if the authoring student (copyright holder) agrees, or, if the thesis was written by a team of students, if all the co-authors (copyright holders) agree. After a thesis is published on the HSE website, it obtains the status of an online publication.

Student theses are objects of copyright and their use is subject to limitations in accordance with the Russian Federation’s law on intellectual property.

In the event that a thesis is quoted or otherwise used, reference to the author’s name and the source of quotation is required.

Search all student theses