Computational Analyses/Pipeline for Identification of Molecular Markers from Genomic Sequences

McMaster University Published: October 13, 2020
Hamilton, Ontario
Internship Type
Salary range
$15-20 per hour
Hours per week
Start Date
End Date


Advances in DNA sequencing technology now permit obtaining in-depth sequence information from any clinical or environmental sample, rapidly and at low cost. The entire collection of DNA sequences from any sample, referred to as a metagenome, can now be examined for the presence of either all organisms or specific organisms. These developments will have a transforming effect on the practise of microbiology, specifically clinical diagnostics, in the coming years. However, the efficient probing of vast amount of sequence data present in a metagenome requires novel reductive approaches which can rapidly and reliably detect the presence of specific organisms in large datasets. Our earlier work on genome sequences have identified two different types of DNA signature sequences, referred to as Conserved Signature Proteins (CSPs) and Conserved Signature Insertions/deletions (CSIs), which are highly specific characteristics of particular organisms. These CSIs and CSPs due to their high degree of specificity for particular organisms provide novel and reliable means for the detection of specific organisms in metagenomic sequences. In this project, the intern will be involved in the development of new softwares for efficiently identifying CSIs and CSPs for additional groups of microbes to expand the current dataset. In addition, he will also participate in the development of a computational pipeline which using our database of CSIs and CSPs can detect the presence of any matches to these markers in genomic sequences.

Duties and responsibilities

The intern will be trained in analyzing genome sequences using different bioinformatic tools.  His/her duties will include i) Using NCBI server for obtaining sequence information for specific genes/proteins or entire genomes, different types of BLAST searches and their applications; ii) Creation of multiple sequence alignments using CLUSTALx, MUSCLE and MEGA programs: iii) Identify molecular signatures such as conserved signature indels and conserved signature proteins using a number of software viz. SigFinder, SigCreate, SigStyle, etc. developed in my lab; iv) Develop a computational software pipeline integrating different steps involved in the identification of molecular signatures: v) writing a report on the results of these studies for publication

Knowledge and skills

Intern should possess:

  1. Good writing skills
  2. Good background knowledge of microbiology and genomics
  3. Ability to write software programs of introductory complexity using programming languages such as Java, C++, Python.
  4. Ability to efficiently work with Microsoft Word, PowerPoint, Excel, GraphPad Prism, Adobe Photoshop
  5. Good time-management and ability to organize large amount of data

Education required

Preferably a B.Sc. or M.Sc. degree in biological sciences. Candidates with degree in software engineering but with good background knowledge of biological sciences will also be well-suited for this position. Senior undergraduate students, in a degree program in Biochemistry, Biology, Microbiology or software engineering who are looking for co-op work position, will also be considered for this position.

Certification required


Eligibility criteria

Career-Launcher Internships are funded by the Government of Canada under the Youth Employment Strategy. For program criteria information visit their website.


Qualified interns are:

  • Post-secondary students and graduates
  • No more than 30 years of age at the start of the internship
  • Canadian citizens, permanent residents or persons granted refugee status in Canada*
  • Legally allowed to work according to the relevant provincial and Canadian legislation and regulations
  • Available to work for at least six months
  • Not previous participants of a federal youth employment program
  • Not employees of the hiring employer prior to the start of their internship (does not apply to previous coop students or student interns)

*Refugee protection must be conferred under the Immigration and Refugee Protection Act. Persons awaiting refugee status, as well as those who hold a temporary visitor visa, student visa or work visa, are ineligible to participate in a Youth Employment Strategy initiative.

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