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 /> <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>To apply for this project you will need to make a formal application for research degree study through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University website</a>. You will need to create a login ID with a username and PIN. </p> <p>•    For <strong>Application type</strong> please select <strong>Research Degrees – Research Postgraduate</strong>. <br /> •    The admission year for this project is <strong>2027/28</strong> Academic Year. <br /> •    You will need to select your <strong>Planned Course of Study</strong> from a drop-down menu. For this project, scroll down and select <strong>PHP Statistics Full Time.</strong> <br /> •    The project start date for this project is <strong>1 October 2027</strong>, please use this as your <strong>Proposed Start Date of Research</strong>. <br /> •    Please state clearly in the<strong> Research Information Section</strong> that the research degree you wish to be considered for is <strong>Fast algorithms for efficient biosequence search</strong> 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.</p> <p><strong>Please state clearly in the Finance section</strong>, <strong>the funding that you are applying for, if you are self-funding or externally sponsored</strong>.</p> <p>More information on how to apply is available on our website <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">here</a>. You will be required to provide a personal statement which outlines your interest in the project you are applying for, why you have chosen it and how your skills map onto the requirements of the project.</p> <p>We will assess applications continuously as we receive them. We welcome and strongly encourage any potential applicants to contact the supervisor(s) for an informal discussion, prior to applying, and recommend submitting your application early.</p> <p><strong>If you are applying 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 including the grading scheme</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> </ul> <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>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<p>This is a non funded PhD project. Applicants are expected to be self funded or to secure external funding.</p> <p>You can find out more about our Funding Opportunities on our <a href="https://phd.leeds.ac.uk/">Postgraduate Research Opportunities</a> website.</p> <p><strong>Important: </strong>Please note that all costs associated with your arrival at Leeds (<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>For questions related to the application process and eligibility, please contact PGR Admissions by email to <a href="mailto:epspgradmissions@leeds.ac.uk">epspgradmissions@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>