scholarly journals Computational Tools for Identification of microRNAs in Deep Sequencing Data Sets

10.5772/21173 ◽  
2011 ◽  
Author(s):  
Manuel A. S. Santos ◽  
Ana Raquel
Keyword(s):  
Deep Sequencing ◽  
Data Sets ◽  
Sequencing Data ◽  
Computational Tools ◽  
Deep Sequencing Data

scholarly journals Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies

2018 ◽  
Author(s):  
Juanita Pang ◽  
Cristina Venturini ◽  
Asif U. Tamuri ◽  
Sunando Roy ◽  
Judith Breuer ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Evolutionary Dynamics ◽  
Synthetic Data ◽  
Data Sets ◽  
Haplotype Reconstruction ◽  
Sequencing Data ◽  
New Approach ◽  
Deep Sequencing Data ◽  
Genomic Element ◽  
Haplotype Assignment

ABSTRACTLongitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.

scholarly journals GenomeGems: evaluation of genetic variability from deep sequencing data

2012 ◽  
Vol 5 (1) ◽  
pp. 338
Author(s):  
Sharon Ben-Zvi ◽  
Adi Givati ◽  
Noam Shomron
Keyword(s):  
Genetic Variability ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data

2017 ◽  
Vol 26 ◽  
pp. 1-11 ◽  
Author(s):  
Molly M. Rathbun ◽  
Jennifer A. McElhoe ◽  
Walther Parson ◽  
Mitchell M. Holland
Keyword(s):  
Dna Damage ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 297-310 ◽  
Author(s):  
Xiaozeng Yang ◽  
Lei Li
Keyword(s):  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16403 ◽  
Author(s):  
Seongho Ryu ◽  
Natasha Joshi ◽  
Kevin McDonnell ◽  
Jongchan Woo ◽  
Hyejin Choi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Sequencing ◽  
Human Breast Cancer ◽  
Secondary Structures ◽  
Human Breast ◽  
Sequencing Data ◽  
Deep Sequencing Data

Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

2016 ◽  
Vol 37 (12) ◽  
pp. 1283-1298 ◽  
Author(s):  
Dario Veneziano ◽  
Sebastiano Di Bella ◽  
Giovanni Nigita ◽  
Alessandro Laganà ◽  
Afredo Ferro ◽  
...  
Keyword(s):  
Data Analysis ◽  
Deep Sequencing ◽  
Noncoding Rna ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Sequencing Data Analysis

Deep Sequencing Data Analysis

2018 ◽  
Vol 15 (2) ◽  
pp. 482-483
Author(s):  
Bijoy K. Ghosh ◽  
Aniruddha Datta ◽  
Ranadip Pal
Keyword(s):  
Data Analysis ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Sequencing Data Analysis
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