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Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

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.

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Related Experiment Video

Updated: May 26, 2026

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

Efficient de novo assembly of large genomes using compressed data structures.

Jared T Simpson¹, Richard Durbin

¹Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Genome Research

|December 14, 2011

Summary

String Graph Assembler (SGA) is a new tool for de novo genome assembly. It efficiently assembles large genomes with low memory, making it practical for standard computing clusters.

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Novel Sequence Discovery by Subtractive Genomics

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Last Updated: May 26, 2026

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

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Published on: August 20, 2021

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

De novo genome sequence assembly is crucial for characterizing new genomes and unbiased individual sequencing.
Existing assemblers often require substantial computational resources, limiting accessibility.

Purpose of the Study:

To present memory-efficient data structures and algorithms for genome assembly.
To introduce a novel assembler, String Graph Assembler (SGA), based on the FM-index and compressed Burrows-Wheeler transform.

Main Methods:

Developed memory-efficient data structures and algorithms utilizing the FM-index.
Implemented SGA, an overlap-based string graph assembler, designed for parallelization.
Applied algorithms for error correction, assembly, and scaffolding of large sequence datasets.

Main Results:

Successfully assembled 1.2 billion human genome sequence reads using 54 GB of memory.
Achieved highly accurate and contiguous contigs, covering 95% of the reference genome.
Demonstrated SGA's practicality for mammalian-sized genomes on low-end computing clusters due to low memory usage and parallelization.

Conclusions:

SGA offers a practical and memory-efficient solution for de novo genome assembly.
The overlap-based string graph approach and FM-index integration enable efficient large-scale genome analysis.
SGA democratizes genome assembly by enabling its use on accessible computing infrastructure.