scholarly journals LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads

2020 ◽  
Author(s):  
Quang Tran ◽  
Alexej Abyzov
Keyword(s):  
Copy Number Variants ◽  
Supplementary Information ◽  
Segmental Duplications ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Long Reads ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution ◽  
Genomic Structural Variants ◽  
Memory Efficient

Abstract Summary Defining the precise location of structural variations (SVs) at single-nucleotide breakpoint resolution is a challenging problem due to large gaps in alignment. Previously, Alignment with Gap Excision (AGE) enabled us to define breakpoints of SVs at single-nucleotide resolution; however, AGE requires a vast amount of memory when aligning a pair of long sequences. To address this, we developed a memory-efficient implementation—LongAGE—based on the classical Hirschberg algorithm. We demonstrate an application of LongAGE for resolving breakpoints of SVs embedded into segmental duplications on Pacific Biosciences (PacBio) reads that can be longer than 10 kb. Furthermore, we observed different breakpoints for a deletion and a duplication in the same locus, providing direct evidence that such multi-allelic copy number variants (mCNVs) arise from two or more independent ancestral mutations. Availability and implementation LongAGE is implemented in C++ and available on Github at https://github.com/Coaxecva/LongAGE. Supplementary information Supplementary data are available at Bioinformatics online.

Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution

2014 ◽  
Vol 41 (12) ◽  
pp. 653-657 ◽  
Author(s):  
Lei Chen ◽  
Long Jin ◽  
Mingzhou Li ◽  
Shilin Tian ◽  
Tiandong Che ◽  
...  
Keyword(s):  
Wild Boar ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

scholarly journals Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite

2019 ◽  
Vol 36 (7) ◽  
pp. 2033-2039 ◽  
Author(s):  
Junfeng Liu ◽  
Ziyang An ◽  
Jianjun Luo ◽  
Jing Li ◽  
Feifei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Quantitative Estimation ◽  
Supplementary Information ◽  
Biological Processes ◽  
Single Nucleotide ◽  
Rna Immunoprecipitation ◽  
Nucleotide Resolution ◽  
Human And Mouse ◽  
Single Nucleotide Resolution

Abstract Motivation RNA 5-methylcytosine (m5C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m5C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m5C in splicing remains to be elucidated due to lack of isoform level m5C quantification tool. Results We developed a computational package to quantify Epitranscriptomal RNA m5C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m5C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m5C is not evenly distributed among the transcript isoforms, implying the m5C may subject to be regulated at isoform level. Availability and implementation Episo is released under the GNU GPLv3+ license. The resource code Episo is freely accessible from https://github.com/liujunfengtop/Episo (with Tophat/cufflink) and https://github.com/liujunfengtop/Episo/tree/master/Episo_Kallisto (with Kallisto). Supplementary information Supplementary data are available at Bioinformatics online.

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads

2019 ◽  
Vol 35 (16) ◽  
pp. 2859-2861
Author(s):  
Linfang Jin ◽  
Jinhuo Lai ◽  
Yang Zhang ◽  
Ying Fu ◽  
Shuhang Wang ◽  
...  
Keyword(s):  
Gene Fusion ◽  
Source Code ◽  
High Sensitivity ◽  
Supplementary Information ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution ◽  
Fusion Detection ◽  
Better Than

AbstractSummaryHere we developed a tool called Breakpoint Identification (BreakID) to identity fusion events from targeted sequencing data. Taking discordant read pairs and split reads as supporting evidences, BreakID can identify gene fusion breakpoints at single nucleotide resolution. After validation with confirmed fusion events in cancer cell lines, we have proved that BreakID can achieve high sensitivity of 90.63% along with PPV of 100% at sequencing depth of 500× and perform better than other available fusion detection tools. We anticipate that BreakID will have an extensive popularity in the detection and analysis of fusions involved in clinical and research sequencing scenarios.Availability and implementationSource code is freely available at https://github.com/SinOncology/BreakID.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

FEBS Letters ◽  
1988 ◽  
Vol 234 (2) ◽  
pp. 295-299 ◽  
Author(s):  
M. Vojtíšková ◽  
S. Mirkin ◽  
V. Lyamichev ◽  
O. Voloshin ◽  
M. Frank-Kamenetskii ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Supercoiled Dna ◽  
Chemical Probing ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution
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