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Related Concept Videos

Genome Annotation and Assembly03:36

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.
RNA-seq03:21

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 microarray-based...

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Related Experiment Video

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Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

Pei Li1, Guoli Ji, Min Dong

  • 1Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.

Bioinformatics (Oxford, England)
|July 14, 2012
PubMed
Summary

We developed CBrowse, a web-based tool for visualizing and analyzing transcriptomics data from non-model organisms. This application helps examine assembly quality, polymorphisms, and sequencing errors in transcriptome projects.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Transcriptomics data for non-model organisms is rapidly increasing.
  • Efficient tools are needed for analyzing this data.

Purpose of the Study:

  • To develop a web browser for visualizing and analyzing transcriptome assemblies and contigs.
  • To facilitate the examination of assembly quality, genetic polymorphisms, sequence repeats, and sequencing errors.

Main Methods:

  • Developed CBrowse, an AJAX-based web browser.
  • Utilized a three-tier architecture and a data pre-processing pipeline.
  • Input: FASTA and SAM/BAM files; Output: image, JSON, CSV files.

Main Results:

  • CBrowse offers integrated web interfaces for data navigation, sorting, filtering, and searching.
  • The pre-processing pipeline detects polymorphisms, SSRs, and sequencing errors.
  • Generated files are directly usable by web interfaces for smooth data visualization.

Conclusions:

  • CBrowse is a versatile tool for transcriptome sequencing projects.
  • It aids in the close examination of assembly quality and potential sequence anomalies.
  • Facilitates efficient analysis of large transcriptomics datasets for non-model organisms.