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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Genome information management and integrated data analysis with HaloLex.

Friedhelm Pfeiffer¹, Alexander Broicher, Thomas Gillich

¹Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Archives of Microbiology

|July 2, 2008

Summary

HaloLex software aids in managing and visualizing microbial omics data. It improves gene prediction accuracy, especially for GC-rich genomes, by integrating genomic and proteomic information.

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Last Updated: Jul 4, 2026

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Published on: June 28, 2018

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Managing and analyzing microbial omics data presents challenges, particularly for GC-rich genomes.
Standard gene finders struggle with accurate gene prediction and start codon assignment in these genomes due to low stop codon abundance.

Purpose of the Study:

To introduce HaloLex, a software system for central management, integration, curation, and web-based visualization of microbial omics data.
To demonstrate HaloLex's utility in improving gene prediction and start codon assignment by integrating genomic and proteomic data.

Main Methods:

Developed and applied the HaloLex software system for central data management and analysis.
Integrated genome-wide proteomic results with underlying genomic data for manual curation of haloarchaeal genomes.
Utilized homology-based methods for gene discovery and start codon correction.

Main Results:

Successfully curated three haloarchaeal genomes (Halobacterium salinarum, Natronomonas pharaonis, Haloquadratum walsbyi) using HaloLex.
Enhanced the reliability of start codon assignment for Halobacterium salinarum through proteomic identification of N-terminal peptides.
Detected 47 previously unidentified genes and corrected over 300 start codon misassignments in Haloarcula marismortui.

Conclusions:

HaloLex is an effective tool for managing, integrating, and visualizing microbial omics data.
The integration of proteomic data significantly improves gene prediction accuracy and start codon assignment in challenging GC-rich genomes.
HaloLex facilitates the discovery of novel genes and correction of errors in existing genome annotations.