scholarly journals High Quality de novo Sequencing and Assembly of the Saccharomyces Arboricolus Genome

2014 ◽  
pp. 313-340
Keyword(s):  
De Novo ◽  
De Novo Sequencing ◽  
High Quality

scholarly journals High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 69 ◽  
Author(s):  
Gianni Liti ◽  
Alex N Nguyen Ba ◽  
Martin Blythe ◽  
Carolin A Müller ◽  
Anders Bergström ◽  
...  
Keyword(s):  
De Novo ◽  
De Novo Sequencing ◽  
High Quality

scholarly journals Complete chloroplast genome of Alternanthera philoxeroides by de novo sequencing

2021 ◽  
Vol 6 (7) ◽  
pp. 1826-1828
Author(s):  
Ping Jiang ◽  
Guangpei Xu ◽  
Yanfei He ◽  
Taotao Sun ◽  
Changli Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
De Novo Sequencing ◽  
Alternanthera Philoxeroides ◽  
Complete Chloroplast Genome

scholarly journals De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

2021 ◽  
Author(s):  
Mathieu Dupré ◽  
Magalie Duchateau ◽  
Rebecca Sternke-Hoffmann ◽  
Amelie Boquoi ◽  
Christian Malosse ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Light Chain ◽  
De Novo ◽  
De Novo Sequencing

scholarly journals De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1342
Author(s):  
Shaghayegh Mehravi ◽  
Gholam Ali Ranjbar ◽  
Ghader Mirzaghaderi ◽  
Anita Alice Severn-Ellis ◽  
Armin Scheben ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Snps ◽  
The Family ◽  
Double Digestion ◽  
Flanking Sequences ◽  
Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

ON PREPROCESSING AND ANTISYMMETRY IN DE NOVO PEPTIDE SEQUENCING: IMPROVING EFFICIENCY AND ACCURACY

2008 ◽  
Vol 06 (03) ◽  
pp. 467-492 ◽  
Author(s):  
KANG NING ◽  
NAN YE ◽  
HON WAI LEONG
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Computational Models ◽  
De Novo ◽  
Noise Removal ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Tandem Mass ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

Peptide sequencing plays a fundamental role in proteomics. Tandem mass spectrometry, being sensitive and efficient, is one of the most commonly used techniques in peptide sequencing. Many computational models and algorithms have been developed for peptide sequencing using tandem mass spectrometry. In this paper, we investigate general issues in de novo sequencing, and present results that can be used to improve current de novo sequencing algorithms. We propose a general preprocessing scheme that performs binning, pseudo-peak introduction, and noise removal, and present theoretical and experimental analyses on each of the components. Then, we study the antisymmetry problem and current assumptions related to it, and propose a more realistic way to handle the antisymmetry problem based on analysis of some datasets. We integrate our findings on preprocessing and the antisymmetry problem with some current models for peptide sequencing. Experimental results show that our findings help to improve accuracies for de novo sequencing.

scholarly journals The Gossypium stocksii genome as a novel resource for cotton improvement

2021 ◽  
Author(s):  
Corrinne E Grover ◽  
Daojun Yuan ◽  
Mark A Arick ◽  
Emma R Miller ◽  
Guanjing Hu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Pest Resistance ◽  
Cotton Leaf ◽  
High Quality ◽  
Cotton Leaf Curl Virus ◽  
Cotton Species ◽  
Wild Cotton ◽  
Leaf Curl Virus ◽  
Insight Into

Abstract Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (G. somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.

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