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Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

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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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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Eukaryotic gene prediction using GeneMark.hmm.

Mark Borodovsky¹, Alex Lomsadze, Nikolai Ivanov

¹School of Biology and School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.

Current Protocols in Bioinformatics

|April 23, 2008

Summary

This summary is machine-generated.

GeneMark.hmm is a tool for finding genes in eukaryotic DNA. It uses sophisticated models to accurately predict gene locations and features, aiding genomic research.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate gene detection is crucial for understanding eukaryotic genome function.
Existing methods may have limitations in sensitivity or specificity for diverse eukaryotic sequences.

Purpose of the Study:

To present eukaryotic GeneMark.hmm as a robust method for gene detection in eukaryotic DNA.
To detail the underlying models and their integration into a Hidden Markov Model (HMM).
To provide guidance on utilizing GeneMark.hmm both online and locally.

Main Methods:

Utilizes Markov models for protein-coding and noncoding sequences.
Incorporates positional nucleotide frequency matrices for start, stop, and splice site prediction.
Integrates sequence models with length distributions of genomic elements (exons, introns, intergenic regions) into a single HMM.

Main Results:

Eukaryotic GeneMark.hmm effectively detects genes in eukaryotic DNA sequences.
The method demonstrates accuracy in predicting key gene features.
GeneMarkS EV is highlighted for its application in eukaryotic viral gene detection.

Conclusions:

Eukaryotic GeneMark.hmm offers a comprehensive approach to gene prediction.
The integrated HMM provides a powerful framework for eukaryotic genome annotation.
Accessible implementation facilitates widespread use in genomic research.