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Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads.  ...  In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  For a comparison of RNA-seq read mappers, see [318] and [319] . ii) BS-seq reads.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq

Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine [article]

Charlotte Brault, Agnès Doligez, Loïc le Cunff, Aude Coupel-Ledru, Thierry Simonneau, Patrice This, Timothée Flutre
2020 bioRxiv   pre-print
Using simulations, we recommend the penalized regression method Elastic Net (EN) as a default for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize  ...  Indeed, penalized methods were more powerful than interval mapping for QTL detection across various genetic architectures.  ...  Acknowledgments We thank Marie Perrot-Dockès for her help concerning penalized regression methods, the South Green platform for computing, notably Bertrand Pitollat, and the GREAT platform, notably Amandine  ... 
doi:10.1101/2020.10.26.355420 fatcat:tbsrtavwu5bt3nclavbcra7ski

Phylogenetic Analysis [chapter]

An Introduction to Computational Biochemistry  
Two scripts for DNA/RNA are ''naba'' and ''separate bases.''  ...  From the base compositions of DNA and RNA given in the following tables, deduce the statistical significance for the statement that the base ratios (A/T(U) and G/C are unity for DNA but vary for RNA (Note  ...  Deduce the probable conformations for the two chains of a hammerhead ribozyme with the following sequences by performing folding analysis, geometry optimization and dynamic simulation (heating to and equilibrate  ... 
doi:10.1002/0471223840.ch13 fatcat:nipg4bxrevau3efb6bagqscufy

Discovering genetic interactions based on natural genetic variation

Marit Ackermann, Technische Universität Dortmund, Technische Universität Dortmund
2012
In this thesis, I propose a method for inferring allele incompatibilities that is exclusively based on DNA sequence information.  ...  Our method detected substantially more imbalanced allele pairs than what we got in simulations assuming no interactions.  ...  Transcription factor target gene identification based on ChIP-seq data. submitted.  ... 
doi:10.17877/de290r-10762 fatcat:7x2xkkgh4bbmzckdvtqmznbcci

Creating artificial sugar isomerases on the scaffold of a monomeric triosephosphate isomerase (A‐TIM) by protein engineering [article]

Mirja Krause, Technische Universität Berlin, Technische Universität Berlin, Peter Neubauer, Rik Wierenga
2014
It was found that the secondary structure changes were minimal and the putative reaction mechanism would be the same as for TIM using the E167 as the critical base.  ...  structure-based rational design approach.  ...  1323 1723 400 AraA Seq P3 and AraA Seq P4 1503 2008 505 Table 16 : 16 epPCR analysis A-TIM library S96P library A178L library I245A library Number of analyzed sequences 20 19  ... 
doi:10.14279/depositonce-3952 fatcat:a2wrgymgpjgfhknhl4sfhnxwaq