Dataset Information

De Novo Assembly of Highly Substituted Morpholines and Piperazines.

ABSTRACT: 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 introduce a versatile de novo synthesis of the morpholine and piperazine rings using multicomponent reaction chemistry. The large scale amenable building blocks can be further substituted at up to four positions, making this a very versatile scaffold synthesis strategy. Our methods thus fulfill the increasing demand for novel building block design and nontraditional scaffolds which previously were not accessible.

SUBMITTER: Patil P

PROVIDER: S-EPMC5348101 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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De Novo Assembly of Highly Substituted Morpholines and Piperazines.

Patil Pravin P Madhavachary Rudrakshula R Kurpiewska Katarzyna K Kalinowska-Tłuścik Justyna J Dömling Alexander A

Organic letters 20170119 3

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 introduce a versatile de novo synthesis of the morpholine and piperazine rings using multicomponent reaction chemistry. The large scale amenable ...[more]

PMID: 28102692

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Project description:BackgroundSeveral standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art assemblers often did not benefit from this pre-correction step. We found that many error correction tools introduce new errors in reads that overlap highly repetitive DNA regions such as low-complexity patterns or short homopolymers, ultimately leading to a more fragmented assembly.ResultsWe propose BrownieCorrector, an error correction tool for Illumina sequencing data that focuses on the correction of only those reads that overlap short DNA patterns that are highly repetitive in the genome. BrownieCorrector extracts all reads that contain such a pattern and clusters them into different groups using a community detection algorithm that takes into account both the sequence similarity between overlapping reads and their respective paired-end reads. Each cluster holds reads that originate from the same genomic region and hence each cluster can be corrected individually, thus providing a consistent correction for all reads within that cluster.ConclusionsBrownieCorrector is benchmarked using six real Illumina datasets for different eukaryotic genomes. The prior use of BrownieCorrector improves assembly results over the use of uncorrected reads in all cases. In comparison with other error correction tools, BrownieCorrector leads to the best assembly results in most cases even though less than 2% of the reads within a dataset are corrected. Additionally, we investigate the impact of error correction on hybrid assembly where the corrected Illumina reads are supplemented with PacBio data. Our results confirm that BrownieCorrector improves the quality of hybrid genome assembly as well. BrownieCorrector is written in standard C++11 and released under GPL license. BrownieCorrector relies on multithreading to take advantage of multi-core/multi-CPU systems. The source code is available at https://github.com/biointec/browniecorrector .

Dataset Information

De Novo Assembly of Highly Substituted Morpholines and Piperazines.

Publications

De Novo Assembly of Highly Substituted Morpholines and Piperazines.

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