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Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Mass Spectrometry of Amines

Mass Spectrometry of Amines

In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule: a molecule with an odd number of nitrogen atoms produces a parent ion with an odd molecular weight. The remaining fragments have an even mass.
Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit...

Mass Spectrometry: Complex Analysis

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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相关实验视频

Updated: Jun 23, 2025

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

CountASAP:一个轻量级,易于使用的Python包,用于处理ASAPseq数据.

Christopher T Boughter¹, Budhaditya Chatterjee², Yuko Ohta²

¹Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.

bioRxiv : the preprint server for biology

|June 21, 2024

概括

此摘要是机器生成的。

CountASAP是一个新的Python包,它将通过测序 (ASAPseq) 选择抗原分析的转化酶可访问的染色质 (ATAC) 转化为FASTQ数据的计数矩阵. 这种工具有助于下游生物信息分析单细胞基因组学和转录基因组学数据.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

相关实验视频

Last Updated: Jun 23, 2025

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

科学领域:

单细胞基因组学和转录基因组学
生物信息学工具开发开发
表观遗传学和细胞表面标志物分析分析.

背景情况:

单细胞测序技术正在快速发展,使更深入的生物学见解成为可能.
通过测序 (ATAC) 结合通过测序 (ASAPseq) 选择抗原分析,可提供多原子单细胞数据.
现有的软件没有专门重新格式化ASAPseq表面标记器FASTQ数据用于下游分析.

研究的目的:

开发一个用户友好的Python包,用于处理ASAPseq FASTQ数据.
为了生成数量矩阵,对于ASAPseq实验的下游生物信息分析至关重要.
弥合多原子单细胞数据集成计算工具的差距.

主要方法:

开发了CountASAP,这是一个用于FASTQ数据重新格式化的Python包.
实现并行读取匹配到细胞标识符和寡头.
确保与标准下游生物信息分析包的兼容性.

主要成果:

CountASAP成功地将ASAPseq FASTQ文件转换为可用的计数矩阵.
该软件包通过并行处理高效地处理大型数据集.
生成的计数矩阵与常见的生物信息学工作流程兼容.

结论:

CountASAP解决了对ASAPseq数据分析专业软件的急需问题.
该工具简化和加快了单细胞多原子数据的处理.
促进ASAPseq技术在生物研究中的更广泛采用和分析.