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1	Study and comparison of next generation sequence algorithms and tools Yates, Heath Landon January 1900 (has links) Master of Science / Department of Computing and Information Sciences / Doina Caragea / This study is a comparison and exploration of next generation sequencing algorithms and tools. A simulation study was done to compare the performance of edgeR, DESeq, and baySeq in detecting differential gene expression. The methods were compared in context of a balanced pairwise design. The simulation results suggest that the methods are compa- rable under the conditions simulated. The study also explored real data comprised of one biological replicate between two treatments. Cufflinks and CummerRBund were used to detect differential gene expression. The visualization results from the real data suggest no differential expression is present. NGS BaySeq EdgeR DESeq Cufflinks Computer Science (0984)
2	Increasing bioinformatics in third world countries : Studies of S.digitata and P.Polymyxa to further bioinformatics in east Africa / Bioinformatiska förbättringsåtgärder för u-länder : Studier av S.digitata och P.Polymyxa för att förbättra bioinformatiken i östra Afrika Isak, Sylvin January 2016 (has links) Despite an increase of biotechnical studies in third world countries, the bioinformatical side is largely lacking. In this paper we attempt to further the bioinformatical capabilities of east Af-rica. The project consisted of two teaching segments for east African doctorates, one as part of an academic workshop at ILRI, Kenya, and one in a small class at SLU, Sweden. The project also included the generation of two simple to use bioinformatical pipelines with the explicit aim to be reused by novice bioinformaticians from the very same region. The viability of the piplines were verified by generating transcriptional expression level differences for Paeni-bacillus polymyxa strain A26 and whole genome annotations for Setaria digitata. Both pipe-lines may have some merit for the collaborative effort between ILRI and SLU to annotate Eleusine coracana, a draught resilient crop, the annotation of which may save lives. The teaching material, source code for the pipelines and overall teaching impression have been included in this paper. bioinformatics pipeline Setaria digitata Paenibacillus polymyxa Eleusine coracana annotation expression level east Africa eBioKit MAKER Cufflinks third world country genome transcriptome Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi)

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Study and comparison of next generation sequence algorithms and tools

Increasing bioinformatics in third world countries : Studies of S.digitata and P.Polymyxa to further bioinformatics in east Africa / Bioinformatiska förbättringsåtgärder för u-länder : Studier av S.digitata och P.Polymyxa för att förbättra bioinformatiken i östra Afrika