Identifying mirnas in RNA viruses

Transcription

1 1 / 13 Identifying mirnas in RNA viruses Kevin Lamkiewicz Friedrich Schiller Universität Jena nd TBI Winterseminar Bled

2 2 / 13 mirnas and their function U C A C A G G U C A A G C G U U G G U C A U C U G U C C A G U U C G C A A C C A G U A G U C C C G A G C G G A C U hairpin structure (precursor structure) mature mirna: 18-21nt regulatory function on post-transcriptonal level

3 3 / 13 mirnas in Viruses

4 3 / 13 mirnas in Viruses Isaac W Boss, Rolf Renne Viral mirnas: tools for immune evasion; Current Opinion in Microbiology (2010)

5 3 / 13 mirnas in Viruses Isaac W Boss, Rolf Renne Viral mirnas: tools for immune evasion; Current Opinion in Microbiology (2010)

6 4 / 13 Goals Short-Term use existing tools to identify known mirnas analyze novel mirnas

7 4 / 13 Goals Short-Term use existing tools to identify known mirnas analyze novel mirnas Long-Term de-novo viral (pre-)mirna prediction systematic overview of mirnas encoded by RNA viruses

8 5 / 13 Datasets and Tools

9 6 / 13 small RNA-Seqs

10 6 / 13 small RNA-Seqs

11 6 / 13 small RNA-Seqs small RNA-Seq

12 7 / 13 mirna Detection Tools raw-reads pre-processing processed reads individual candidates mirna prediction tools mapped reads intersection of candidate sets candidates

13 8 / 13 Progress

14 9 / 13 First Results raw-reads pre-processing processed reads individual candidates mirna prediction tools mapped reads intersection of candidate sets candidates

15 10 / 13 First Results mirdeep2 and HHMMiR mirdeep2 detected annotated mirnas of BLV HHMMiR predicted novel mirnas in turnip crinkle virus (TCV)

16 10 / 13 First Results mirdeep2 and HHMMiR mirdeep2 detected annotated mirnas of BLV HHMMiR predicted novel mirnas in turnip crinkle virus (TCV) However: Tools that uses machine learning methods and classifiers are trained against a specific model (Homo sapiens, Arabidopsis thaliana, etc...)

17 11 / 13 Outlook Next steps Gather more data Get other tools running Triplet-SVM, NovoMIR, ncpro-seq, CoRaL, mipred, mireader, miranalyzer,...

18 11 / 13 Outlook Next steps Gather more data Get other tools running Triplet-SVM, NovoMIR, ncpro-seq, CoRaL, mipred, mireader, miranalyzer,... Compare results of different tools Understand differences in the results (If there are any)

19 Idea & Project Datasets and Tools Progress 12 / 13

20 13 / 13 Thank you for your attention! (Images from clipartpanda.com and clipartkid.com)

21 14 / 13 Host-Virus Dataset Host Virus A. thaliana Turnip crinkle virus (TCV) Sheep Bovine leukemia virus (BLV) Human Enterovirus 71 (EV71) Human Coxsackievirus A16 (CA16) Potato Potato virus Y (PVY) Soybean Soybean mosaic virus (SMV) Steer Bovine foamy virus (BFV) Mosquito Chikungunya virus (CHIKV) Appletree Apple Stem Grooving Virus (ASGV) Human HIV1 Bat Ebola virus Hamster West-Nile virus (WNV) Mosquito Dengue virus

22 15 / 13 Host-Virus Dataset Host Virus Cucumis melo Melon necrotic spot virus Nicotiana benthamiana Cymbidium ring spot virus A. thaliana Tobacco rattle virus A. thaliana Cucumber mosaic virus Nicotiana benthamiana Pepper mild mottle virus Cucumis melo Watermelon mosaic virus A. thaliana Turnip mosaic virus Nicotiana benthamiana Potato virus X Solanum lycopersicum Tomato yellow leaf curl virus