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

McMaster University Publié : le 13 Oct 2020
Lieu
Hamilton, Ontario
Échelle salariale
$15-20 per hour
Heures par semaine
35
Date de début
2020/11/02
Date de fin
2021/04/30

Description

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.

Tâches et responsabilités

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

Connaissances et compétences

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

Scolarité requise

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.

Certifications requises

None

Eligibility criteria

Les Stages lancement de carrière sont financés par le gouvernement du Canada dans le cadre de la Stratégie emploi jeunesse. Pour des renseignements sur les critères d’admissibilité du programme visitez leur site Web.

 

Les stagiaires admissibles :

  • Sont étudiants ou diplômés d’un programme postsecondaire
  • Sont âgés de 30 ans ou moins au début du stage
  • Sont citoyens canadiens, résidents permanents ou détenteurs du statut de réfugié au Canada*
  • Sont légalement autorisés à travailler en vertu des lois et règlements provinciaux et fédéraux applicables
  • Sont disponibles à travailler pendant au moins six mois
  • N’ont pas déjà participé à un programme fédéral d’emploi pour les jeunes
  • N’ont pas été employés par l’employeur avant le début du stage (ne s’appliquent pas aux placements ou stages étudiants antérieurs)

*Le statut de réfugié doit être conféré aux termes de la Loi sur l’immigration et la protection des réfugiés. Les personnes en attente du statut de réfugié et celles qui détiennent un visa de séjour temporaire, visa d’étudiant ou permis de travail, ne peuvent participer à une initiative de la Stratégie emploi jeunesse.

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