From the DNA sequencer to a sequence assembly

2006 ◽  
Author(s):  
J. Bonfield
Keyword(s):  
Sequence Assembly ◽  
Dna Sequencer

A Roadmap to Sequence Assembly Evaluation Tools

2020 ◽  
Vol 15 ◽  
Author(s):  
Sara El-Metwally ◽  
Eslam Hamouda ◽  
Mayada Tarek
Keyword(s):  
Data Analysis ◽  
Evaluation Process ◽  
Sequence Assembly ◽  
Assessment Tools ◽  
Accurate Information ◽  
End User ◽  
Evaluation Tools ◽  
Assembly Evaluation ◽  
Assembly Pipeline ◽  
Evaluation Approaches

: The assembly evaluation process is the starting step towards meaningful downstream data analysis. We need to know how much accurate information is included in an assembled sequence before going further to any data analysis stage. Four basic metrics are targeted by different assembly evaluation tools: contiguity, accuracy, completeness, and contamination. Some tools evaluate these metrics based on comparing the assembly results to a closely related reference. Others utilize different types of heuristics to overcome the missing of a guiding reference, such as the consistency between assembly results and sequencing reads. In this paper, we discuss the assembly evaluation process as a core stage in any sequence assembly pipeline and present a roadmap that is followed by most assembly evaluation tools to assess different metrics. We highlight the challenges that currently exist in the assembly evaluation tools and summarize their technical and practical details to help the end-users choose the best tool according to their working scenarios. To address the similarities/differences among different assembly assessment tools, including their evaluation approaches, metrics, comprehensive nature, limitations, usability and how the evaluated results are presented to the end-user, we provide a practical example for evaluating Velvet assembly results for S. aureus dataset from GAGE competition. A Github repository (https://github.com/SaraEl-Metwally/Assembly-Evaluation-Tools) is created for evaluation result details along with their generated command line parameters.

scholarly journals Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 518
Author(s):  
Zequn Chen ◽  
Xiwu Qi ◽  
Xu Yu ◽  
Ying Zheng ◽  
Zhiqi Liu ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Essential Oils ◽  
Gene Family ◽  
Genome Sequence ◽  
Sequence Assembly ◽  
Terpene Synthase ◽  
Genome Sequence Assembly ◽  
Mentha Longifolia ◽  
Specific Expansion ◽  
Species Specific

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

scholarly journals High-Resolution Analysis of the 5′-End Transcriptome Using a Next Generation DNA Sequencer

PLoS ONE ◽  
2009 ◽  
Vol 4 (1) ◽  
pp. e4108 ◽  
Author(s):  
Shin-ichi Hashimoto ◽  
Wei Qu ◽  
Budrul Ahsan ◽  
Katsumi Ogoshi ◽  
Atsushi Sasaki ◽  
...  
Keyword(s):  
High Resolution ◽  
Next Generation ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Dna Sequencer

scholarly journals New advances in sequence assembly

2017 ◽  
Vol 27 (5) ◽  
pp. xi-xiii ◽  
Author(s):  
Adam M. Phillippy
Keyword(s):  
Sequence Assembly

scholarly journals HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly

BMC Genomics ◽  
2014 ◽  
Vol 15 (S10) ◽  
Author(s):  
Basir Shariat ◽  
Narjes Sadat Movahedi ◽  
Hamidreza Chitsaz ◽  
Christina Boucher
Keyword(s):  
Sequence Assembly ◽  
Selection Of

scholarly journals GlycoFibroTest Is a Highly Performant Liver Fibrosis Biomarker Derived from DNA Sequencer-based Serum Protein Glycomics

2009 ◽  
Vol 8 (5) ◽  
pp. 986-994 ◽  
Author(s):  
Dieter Vanderschaeghe ◽  
Wouter Laroy ◽  
Erwin Sablon ◽  
Philippe Halfon ◽  
Annelies Van Hecke ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Serum Protein ◽  
Dna Sequencer
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