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Related Experiment Video

Updated: Jun 28, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

PEDANT covers all complete RefSeq genomes.

Mathias C Walter¹, Thomas Rattei, Roland Arnold

¹Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.

Nucleic Acids Research

|October 23, 2008

Summary

This summary is machine-generated.

The PEDANT genome database offers comprehensive bioinformatics annotation for over 3000 genomes and 4.5 million proteins. Its enhanced processing pipeline ensures immediate analysis of newly sequenced genomes.

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Comprehensive genome annotation is crucial for understanding biological functions.
Existing annotation pipelines can be time-consuming, delaying the analysis of new genomic data.

Purpose of the Study:

To present the PEDANT genome database and its updated processing pipeline.
To provide a freely accessible resource for extensive genome annotation.

Main Methods:

Utilized a broad set of bioinformatics algorithms for protein and genome annotation.
Integrated the Similarity Matrix of Proteins (SIMAP) database to accelerate processing.
Covered all completely sequenced genomes from the NCBI's Reference Sequence (RefSeq) collection.

Main Results:

Annotated nearly 3000 eukaryotic, eubacterial, archaeal, and viral genomes.
Annotated over 4.5 million proteins.
Achieved an order-of-magnitude speedup in the processing pipeline, enabling real-time analysis of new genomes.

Conclusions:

PEDANT provides a valuable, up-to-date, and efficiently processed resource for genome annotation.
The database facilitates immediate analysis of newly available genomic data for the research community.
Freely accessible via web and web services for academic users.