Agriculture and Bioresources
Crop Development Centre, Department of Plant Sciences
Informatics/Bioinformatics Researcher (Two year Engineer position in Informatics/Bioinformatics)
This position is funded by a research grant administered by the University of Saskatchewan under the direction of Dr. C Pozniak, Crop Development Centre, College of Agriculture and Bioresources.
In support of the international effort (IWGSC - http://www.wheatgenome.org/)to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline (http://www.clermont.inra.fr/triannot). Its modular architecture allows for the annotation and masking of transposable elements, the structural and functional annotation of protein-coding genes with an evidence-based quality indexing, and for identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in 26 hours. It is accessible through a web interface for small scale analyses (< 100 sequences of 3Mb max) or through a server for large scale annotations (thousands of scaffolds). The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 additional genes based on new biological evidence, increasing the percentage of perfect gene prediction to 63%. TriAnnot was designed specifically for complex genomes like wheat, and systematically showed a higher fitness than other annotation pipelines. TriAnnot is easily adaptable to the annotation of other plant genomes, and should become a useful resource for the annotation of large and complex genomes in the future.
However, there is a need for further improvements:
- Build a virtual machine of the TriAnnot pipeline;
- Improve the Gene modeling process - definitely make a choice between two combiners: Eugene and Augustus;
- Incorporate new, well trained ab initio gene prediction programs;
- Develop tools to display splicing variants;
- Implement a module for the discovery of SNP markers;
- Develop and incorporate three new panels:
- mapping the gene models on selected genome models
- mapping the gene models within a pre-calculated phylogeny tree
- mapping the gene models within a known? biological pathways;
- evaluate the possibility to develop a “bogas-like” interface for wheat manual curation (see http://bioinformatics.psb.ugent.be/webtools/bogas/).
Building a virtual machine is a high priority as the improved TriAnnot pipeline will be installed as a mirror site to improve the informatics infrastructure in Canada. In this respect, we would develop a collaboration with iPlant to install the TriAnnot virtual machine (TriAnnot-VM) within the iPlant cyber infrastructure located in the USA. Collaborations are already underway with the CNRS at Roscoff (C. Caron) and the IBCP at Lyon (CF. Blanchet) to work on these aspects. The engineer hired for this position will be in contact with these different centers to build the virtual machine.
The development of the “bogas-like” interface will be made in close collaboration with the VIB in Ghent, Belgium.
The candidate will work under the direction of Dr. C. Pozniak, University of Saskatchewan. The successful candidate will spend the first year as a Visiting Scientist in the group "Structure, Function and Evolution of the Wheat Genome" led by C. Feuillet and located at the UMR INRA-UBP GDEC in Clermont-Ferrand (France). She/he will develop her/his project in direct collaboration with P. Leroy, the research engineer in charge of the TriAnnot project in the group. She/he will interact with researchers and graduate students that are users of the pipeline. She/he will also interact with other groups involved in Genetics, Bioinformatics and with other international laboratories developing similar activities.
In the second year of the project, the candidate will work at the Crop Development Centre, University of Saskatchewan, Canada in the research group led by Dr. Pozniak She/he will install and test the TriAnnot Virtual machine within the informatics infrastructure available at the University of Saskatchewan and use it to annotate the sequence of wheat chromosomes being sequenced by that group. The second year of the project will involve interaction with iPlant to install the TriAnnot virtual machine within the iPlant cyber infrastructure in US. The successful candidate will also assist with writing and preparation of manuscripts for publication.
Qualifications: The candidate must have a minimum of a Master’s degree in computer science or a related field with at least three years of bioinformatics experience. The candidate should have good knowledge in Perl, python and Object Programming. Previous experience of Perl Object Oriented Programming is recommended. Candidate has to be familiar with parallel programming (Cluster) and Cloud computing. Research experience in plant genomics is desirable.
Applicant must have a clear evidence of productivity, creativity and independence; excellent communication skills, and must be proficient in both reading and writing in the English language and an ability to work both independently and within a team. Candidates must have demonstrated report writing and publication capabilities.
Salary: A competitive salary is available with full benefits (pension, health and dental, life insurance). Salary will be commensurate with experience.
Contacts: Parties interested in the position should provide by email a letter of application, Curriculum Vitae with a publication list, a brief statement of research and interests, and the names and contact information for at least three references, to:
Genome Prairie, Senior Project Manager
University of Saskatchewan
Review of applications will begin September 15th, 2012 and continue until the position is filled. All applicants will be notified shortly thereafter. Preferred start date November 1st, 2012.
The University of Saskatchewan is strongly committed to a diverse and inclusive workplace that empowers all employees to reach their full potential. All members of the university community share a responsibility for developing and maintaining an environment in which differences are valued and inclusiveness is practiced. The university welcomes applications from those who will contribute to the diversity of our community. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.