Results 31 to 40 of about 59,976,998 (309)

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

BMC Genomics, 2018
Background De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera ‘Sultanina’ genome assemblies for comparison with the inbred V. vinifera (
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y. Fennell   +5 more
doaj   +1 more source

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. [PDF]

PLoS ONE, 2013
Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects ...
Aarti Desai, Veer Singh Marwah, Akshay Yadav, Vineet Jha, Kishor Dhaygude, Ujwala Bangar, Vivek Kulkarni, Abhay Jere   +7 more
doaj   +1 more source

DOGS: reaction-driven de novo design of bioactive compounds [PDF]

, 2012
We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds.
Ewgenij Proschak (34926), Miriam Walter (185090), Matthias Rupp (185094), Sascha Weggen, Gisbert Schneider, Holger Stark, Felix Reisen (185098), Gisbert Schneider (17096), Miriam Walter, Matthias Rupp, Ewgenij Proschak, Reisen, Felix, Sascha Weggen (185102), Proschak, Ewgenij, Markus Hartenfeller (185082), Walter, Miriam, Hartenfeller, Markus, Holger Stark (4694), Schneider, Gisbert, Rupp, Matthias, Stark, Holger, Zettl, Heiko, Markus Hartenfeller, Heiko Zettl (185086), Felix Reisen, Weggen, Sascha, Heiko Zettl   +26 more
core   +2 more sources

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies [PDF]

PeerJ, 2017
Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp   +5 more
doaj   +2 more sources

De Novo Repeat Classification and Fragment Assembly [PDF]

Genome Research, 2004
Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats.
Pavel A, Pevzner, Paul A, Pevzner, Haixu, Tang, Glenn, Tesler   +3 more
openaire   +2 more sources

Tedna: a transposable element de novo assembler [PDF]

Bioinformatics, 2014
Abstract Motivation : Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain high proportions of transposable elements, and transposable elements appear to be a major force behind ...
Zytnicki, Matthias, Akhunov, Eduard, Quesneville, Hadi   +2 more
openaire   +4 more sources

Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

Genomics Data, 2015
Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence.
Kiran Gopinath Bankar, Vivek Nagaraj Todur, Rohit Nandan Shukla, Madavan Vasudevan   +3 more
doaj   +1 more source

De novo assembly of highly diverse viral populations [PDF]

BMC Genomics, 2012
Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be ...
Yang Xiao, Charlebois Patrick, Gnerre Sante, Coole Matthew G, Lennon Niall J, Levin Joshua Z, Qu James, Ryan Elizabeth M, Zody Michael C, Henn Matthew R   +9 more
openaire   +3 more sources

Metassembler: merging and optimizing de novo genome assemblies [PDF]

Genome Biology, 2015
Abstract Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior ...
Hernandez Wences, Alejandro, Schatz, Michael   +1 more
openaire   +2 more sources

De Novo Assembly of Highly Substituted Morpholines and Piperazines [PDF]

Organic Letters, 2017
The morpholine and piperazine with their remarkable physical and biochemical properties are popular heterocycles in organic and medicinal chemistry used in rational property design. However, in the majority of cases these rings are added to an existing molecule in a building block approach thus limiting their substitution pattern and diversity. Here we
Patil, Pravin; Madhavachary, Rudrakshula; Kurpiewska, Katarzyna; Kalinowska-Tluscik, Justyna; Domling, Alexander   +5 more
openaire   +4 more sources