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Related Experiment Video

Updated: May 31, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Improving pan-genome annotation using whole genome multiple alignment.

Samuel V Angiuoli¹, Julie C Dunning Hotopp, Steven L Salzberg

¹Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. angiuoli@umiacs.umd.edu

BMC Bioinformatics

|July 2, 2011

Summary

This summary is machine-generated.

Genome annotation errors are common, especially in bacterial pan-genomes. Mugsy-Annotator, a new tool, identifies and helps correct these issues by comparing gene structures and suggesting improved annotations.

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Last Updated: May 31, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Advances in sequencing technology enable rapid genome annotation and pan-genome comparisons.
Genome annotations often contain inconsistencies and errors, hindering comparative analysis.
There is a need for tools to compare and improve annotation quality across closely related genomes.

Purpose of the Study:

Introduce Mugsy-Annotator, a novel tool for evaluating genome annotation quality.
Identify orthologs and assess annotation consistency in prokaryotic genomes.
Highlight common annotation anomalies and assist re-annotation efforts.

Main Methods:

Utilize whole genome multiple alignment to compare prokaryotic genomes.
Employ Mugsy-Annotator to identify anomalies in annotated gene structures.
Evaluate annotation quality across species pan-genomes.

Main Results:

Mugsy-Annotator effectively identifies orthologs and evaluates annotation quality.
Common anomalies include inconsistently located translation initiation sites and disrupted genes.
These anomalies are prevalent in bacterial pan-genomes, particularly at initiation sites.

Conclusions:

Whole genome multiple alignment is efficient for identifying orthologs and annotation issues in bacterial pan-genomes.
Annotation inconsistencies can inflate perceived genomic variation within a species.
Mugsy-Annotator aids re-annotation by suggesting edits for improved annotation consistency.