Development of efficient algorithms to manipulate genomic regions

Summary

The aim of this project is to develop novel and efficient database algorithms to process genomic data.

Supervisor(s)

Dr Matloob Khushi

Research Location

Westmead - Childrens Medical Research Institute

Program Type

Masters/PHD

Synopsis

Genomic regions consist of three essential fields: chromosome number, start position, and end position, in addition to a number of optional fields. Certain genomic data such as transcription factor binding sites and epigenetic marks are represented as genomic regions. Identifying overlapping and nearby genomic regions is a major objective of genomic studies, but existing methods to archive a large number of datasets in a personalised database lack sophistication and utility. Relational database management systems (RDBMS) provide an easy SQL interface to query data and therefore perform well when searching for and retrieving specific information in a database, however, their performance is very poor when they are used to natively perform arithmetic operations on large datasets.

The aim of the project is to benchmark the performance of various SQL and NoSQL databases, and to develop novel efficient algorithms to perform arithmetic operations on genomic regions natively.

Additional Information

Children's Medical Research Institute (CMRI) is an award-winning state-of-the-art medical research facility, with over 100 full-time scientists dedicated to researching the genes and proteins important for health and human development. The CMRI is supported in part by its key fundraiser Jeans for Genes®. Our scientists are internationally recognised research leaders and foster excellence in postgraduate training. CMRI graduates are highly sought after nationally and internationally.

CMRI is located at Westmead, a major hub for research and medicine in NSW, and is affiliated with the University of Sydney. Easy to access by public transport.

We are looking for top quality students who can prove a dedicated interest and enthusiasm for scientific research.

Candidates may apply for a CMRI PhD Research Award, which exceeds the Australian Postgraduate Awards and NHMRC scholarships in value. Visit the CMRI website for more details

Eligibility:

Honours entry: GPA on track for Honours Class I / IIA
PhD entry: Honours Class I
Suitable for students with an ICT or Engineering background

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Keywords

databases, SQL, NoSQL, RDBMS

Opportunity ID

The opportunity ID for this research opportunity is: 2092

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