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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.

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Updated: May 8, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

PAVIS: a tool for Peak Annotation and Visualization.

Weichun Huang¹, Rasiah Loganantharaj, Bryce Schroeder

¹Biostatistics Branch and the Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, NC 27709, USA.

Bioinformatics (Oxford, England)

|September 7, 2013

Summary

This summary is machine-generated.

PAVIS is a new tool that helps researchers easily interpret ChIP-seq data by annotating and visualizing genomic enrichment. It provides crucial genomic context for peaks, aiding biological discovery.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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Published on: May 22, 2018

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

ChIP-seq experiments generate large datasets of genomic enrichment regions.
Interpreting these regions requires understanding their genomic context and potential functional significance.
Existing tools may lack user-friendliness for non-bioinformaticians.

Purpose of the Study:

To introduce Peak Annotation and Visualization (PAVIS), a web-based tool for annotating and visualizing ChIP-seq peak data.
To provide a user-friendly interface for biological interpretation of genomic enrichment data.
To enable rapid examination and cross-comparison of genomic context for hypothesis generation.

Main Methods:

Development of a web-based tool, PAVIS.
Integration of peak annotation with genomic feature information (TSS, introns, exons, UTRs).
Implementation of dynamic visualization for multiple loci and experiments.

Main Results:

PAVIS associates ChIP-seq peaks with relevant genomic features.
The tool reports relative enrichment P-values for peaks within distinct genomic categories.
PAVIS generates summary plots illustrating the proportion of peaks in each category.
Dynamic visualization of tens to hundreds of loci from multiple experiments is supported.

Conclusions:

PAVIS offers a peak-oriented annotation and visualization system.
The tool facilitates biological interpretation for non-bioinformaticians.
PAVIS supports rapid examination of genomic context, aiding downstream hypothesis generation.