Fast algorithms for efficient biosequence search

DNA sequencing and the following analysis of biosequences become a core procedure for many problems in biological research, such as medical diagnosis, development of target medicine, virology, forensic sciences, etc. Examples of biosequence search include the detection of mutations within human DNA in cancer studies and searching for matching patterns in microbial genomes. <br /> With an ever-increasing volume of data to process, the development of efficient search algorithms becomes of paramount importance.<br /> <br /> Seeding is one of the techniques which is extensively used in biosequence alignment problems to speed up the searching procedure. A few seeding algorithms have been proposed in the past years. The first seeds which have been suggested represent small contiguous matching patterns and explore the seed-and-extend paradigm. Later the idea has been developed into spaced seeds (binary/ternary), allowing mismatches. <br /> <br /> Another technique is k-mers, a set of short matching patterns of length k which is often used in alignment-free methods. <br /> <br /> However, finding optimal seeds/k-mers, which maximize efficiency, is still a topic for study. Usually, efficiency can be assessed as a compromise between the algorithm’s time complexity and its sensitivity (ratio of correctly aligned sequences). Different studies suggest different methods for increasing efficiency. Often the selection is based on a certain probabilistic model and pre-defined properties of seeds.<br /> <br /> In this project, the student will look into the problem of generating optimal seeds/k-mers to improve the efficiency of biosequence searching algorithms. The focus will be made on the development of a mathematical framework to investigate and demonstrate the efficiency of suggested seeds’ structures.<br />

<p style="margin-bottom:11px">It has been shown in [1] that spaced seeds may be more efficient than contiguous seeds. Other designs of seeding strategy have been suggested, such as adaptive seeds and minimisers to speed up the search at the price of decreasing sensitivity.</p> <p>Seeds generators which produce seeds of a certain structure to satisfy given parameters have been proposed in [2] and [3]. The properties of optimal seeds have been investigated in [4] and a list of optimal seeds for predefined structural properties has been suggested.</p> <p>An example of investigating an optimal parameter for k-mers in error correction tools can be found in [5].</p> <p>[1] Keich Uri, Li Ming, Ma Bin, Tromp John, On spaced seeds for similarity search. Discrete Applied Mathematics. <a href="https://doi.org/10.1016/S0166-218X(03)00382-2">https://doi.org/10.1016/S0166-218X(03)00382-2</a></p> <p>[2] Brejová, B., Brown, D. G., & Vinar, T. (2004). Optimal spaced seeds for homologous coding regions. Journal of bioinformatics and computational biology, 1(4), 595–610. <a href="https://doi.org/10.1142/s0219720004000326">https://doi.org/10.1142/s0219720004000326</a></p> <p>[3] Kucherov, G., Noé, L., & Roytberg, M. (2006). A unifying framework for seed sensitivity and its application to subset seeds. Journal of bioinformatics and computational biology, 4(2), 553–569. <a href="https://doi.org/10.1142/s0219720006001977">https://doi.org/10.1142/s0219720006001977</a></p> <p>[4] Valeriy Titarenko, Sofya Titarenko. PerFSeeB: Designing Long High-weight Single Spaced Seeds for Full Sensitivity Alignment with a Given Number of Mismatches, 15 November 2021, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-1051543/v1]</p> <p>[5] Sharma, A., Jain, P., Mahgoub, A. et al. Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing. BMC Bioinformatics 23, 25 (2022). https://doi.org/10.1186/s12859-021-04547-0</p> <p style="margin-bottom:11px"> </p>

<p>Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University's website</a>. Please state clearly in the Planned Course of Study section that you are applying for <em><strong>PHD Statistics FT,</strong></em> in the research information section that the research degree you wish to be considered for is <em><strong>Fast algorithms for efficient biosequence search</strong></em> as well as <a href="https://eps.leeds.ac.uk/faculty-engineering-physical-sciences/staff/10654/dr-sofya-titarenko">Dr Sofya Titarenko</a> as your proposed supervisor and in the finance section, please state clearly <em><strong>the funding that you are applying for, if you are self-funding or externally sponsored</strong></em>.</p> <p>If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below).</p> <p><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability.</em></p> <p class="MsoNoSpacing">Applications will be considered after the closing date.  Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application.  We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed.</p> <p class="MsoNoSpacing"><strong>Please note that you must provide the following documents in support of your application by the closing date of Monday 6 January 2025 if applying for the China Scholarship Council-University of Leeds Scholarship, Monday 3 February 2025 if applying for Leeds Doctoral Scholarship or Tuesday 1 April 2025 for Leeds Opportunity Research Scholarship.</strong></p> <p><strong>If you are applying for the School of Mathematics Scholarship 2025/26, or with external sponsorship or you are funding your own study, please ensure you provide your supporting documents at the point you submit your application:</strong></p> <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> </ul>

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<p style="margin-bottom:12px"><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong> – The <a href="https://phd.leeds.ac.uk/funding/138-leeds-doctoral-scholarship-2025-faculty-of-engineering-and-physical-sciences#:~:text=Key%20facts&text=One%20Leeds%20Doctoral%20Scholarship%20is,rata%20for%20part%2Dtime%20study.">Leeds Doctoral Scholarship</a> <strong>(closing date: Monday 3 February 2025)</strong>, <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> <strong>(closing date: Tuesday 1 April 2025)</strong> and <a href="https://phd.leeds.ac.uk/funding/55-school-of-mathematics-scholarship-2025-26">School of Mathematics Scholarship 2025/26</a> <strong>(open from October 2024)</strong> are available to UK applicants.</p> <p><strong>Non-UK</strong> – <a href="https://phd.leeds.ac.uk/funding/55-school-of-mathematics-scholarship-2025-26">School of Mathematics Scholarship 2025/26</a> <strong>(open from October 2024)</strong> are available to all International applicants.  The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> <strong>(closing date: Monday 6 January 2025)</strong> is available to nationals of China. The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p>You will be responsible for paying the overtime fee in full in your writing up/overtime year (£320 in Session 2024/25), but the scholarship maintenance allowance will continue to be paid for up to 6 months in the final year of award.</p> <p><strong>Important: </strong>Please note that that the award does <em><strong>not</strong></em> cover the costs associated with moving to the UK.  All such costs (<a href="https://www.leeds.ac.uk/international-visas-immigration/doc/applying-student-visa">visa, Immigration Health Surcharge</a>, flights etc) would have to be met by yourself, or you will need to find an alternative funding source. </p> <p>Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.</p>

<p>For general enquiries about your application, please contact PGR Admissions by email to <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions@leeds.ac.uk</a></p> <p>For questions about this research project, please contact Sofya Titarenko by email to <a href="mailto:S.Titarenko@leeds.ac.uk">S.Titarenko@leeds.ac.uk</a></p>