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Genome Annotation and Assembly

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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: Sep 8, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

SPEAR: Systematic ProtEin AnnotatoR.

Matthew Crown¹, Natália Teruel², Rafael Najmanovich²

¹Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.

Bioinformatics (Oxford, England)

|June 13, 2022

Summary

This summary is machine-generated.

We developed Systematic ProtEin AnnotatoR (SPEAR), a tool to rapidly identify SARS-CoV-2 mutations linked to immune escape and increased transmissibility. This real-time analysis aids genomic surveillance efforts globally.

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Last Updated: Sep 8, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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

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Published on: February 10, 2023

Area of Science:

Virology
Genomics
Bioinformatics

Background:

The emergence of SARS-CoV-2 variants necessitates rapid analysis of genomic surveillance data.
Identifying mutations associated with immune escape and altered transmissibility is crucial for public health.

Purpose of the Study:

To introduce Systematic ProtEin AnnotatoR (SPEAR), a tool for real-time annotation and scoring of SARS-CoV-2 variants.
To enable identification of mutations potentially affecting immune escape and ACE2 binding.

Main Methods:

SPEAR is a lightweight and rapid computational tool.
It analyzes mutations at the point of sequencing.
The tool provides interactive data visualization reports.

Main Results:

SPEAR facilitates the identification of mutations linked to potential immune escape.
It scores mutations for their contribution to transmissibility, specifically ACE2 binding.
The tool supports real-time evaluation of genomic surveillance results.

Conclusions:

SPEAR offers a valuable resource for field-based genomic surveillance of SARS-CoV-2.
The tool aids in understanding the evolutionary dynamics of the virus in real time.
SPEAR is freely available and implemented in Python.