PhD Martti Vasar
Research Fellow in Ecoinformatics
martti.vasar [ at ] ut.ee
J. Liivi st. 2- 306
My main goal in the workgroup is in helping to deal with large-scale analysis using different workflows and cluster computers. We mainly use BLAST program to compare different plant roots and organism sequences. In collaboration with other workgroup members we have managed to create workflow to analyze 454 sequence data.
Addition to above, I also help to develop database "EcoBank", which contains various metadata and holds information about samples gathered all over the world. Database is developed in the fashion, that it would be easy to make flexible search engine on it.
During my PhD studies I developed a workflow and a pipeline to analyse sequence data from Illumina sequencing platform and how it compares with other sequencing platforms like 454 sequencing. My doctoral thesis was supervised by PhD Maarja Öpik and Prof. J. Peter W. Young.
Selected papers:
- Vasar M, Davison J, Neuenkamp L, Sepp S‐K, Young JPW, Moora M & Öpik M. (2021), User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13340
- Vasar, M.; Andreson, R.; Davison, J.; Jairus, T.; Moora, M.; Remm M.; Young, J. P. W.; Zobel, M. & Öpik, M. 2017. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza doi: 10.1007/s00572-017-0791-y.
ETIS - García de León, D.; Moora, M.; Öpik, M.; Jairus, T.; Neuenkamp, L.; Vasar, M.; Bueno, C.G.; Gerz, M.; Davison, J. & Zobel, M. 2016. Dispersal of arbuscular mycorrhizal fungi and plants during succession. Acta Oecologica 77: 128-135. ETIS
- Thiery, O.; Vasar, M.; Jairus, T.; Davison, J.; Roux, C.; Kivistik, P.-A.; Metspalu, A.; Milani, L.; Saks, Ü.; Moora, M.; Zobel, M. & Öpik, M. 2016.Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent. Molecular Ecology 25: 2816-2832. ETIS
Developed pipelines:
- SSU pipeline - pipeline consisting series of command line inputs to analyse AM fungal sequences from 454 and Illumina platforms
- gDAT pipeline - enhanced version of the previous pipeline containing graphical interface to analyse AM fungal sequences
