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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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Updated: Jul 13, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Comparing compressed sequences for faster nucleotide BLAST searches.

Michael Cameron¹, Hugh E Williams

¹School of Computer Science and Information Technology, RMIT University, Melbourne, Australia. mcam@cs.rmit.edu.au

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|August 2, 2007

Summary

Scientists can now search nucleotide sequences twice as fast with improved BLASTN algorithms. These enhancements utilize compressed data formats and novel alignment methods for quicker, accurate genomic discovery.

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Last Updated: Jul 13, 2026

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The Basic Local Alignment Search Tool (BLAST) is crucial for analyzing genomic sequences.
BLASTN, the nucleotide variant, lacks detailed algorithmic descriptions and has lagged behind BLASTP in development.
Nucleotide databases are growing rapidly, necessitating faster search capabilities.

Purpose of the Study:

To significantly improve the performance and efficiency of the BLASTN algorithm.
To introduce novel algorithmic approaches for faster nucleotide sequence homology searches.
To enhance the accuracy and speed of gapped alignment in BLASTN.

Main Methods:

Development of compressed, byte-packed formats for query and collection sequences.
Implementation of lookup tables and numeric comparisons for rapid base-pair comparisons.
Introduction of two new, fast gapped alignment schemes that avoid sequence decompression.

Main Results:

The proposed innovations more than double the speed of BLASTN searches.
The improvements maintain the accuracy of sequence alignments.
New algorithms are integrated into a publicly available version of BLAST.

Conclusions:

Optimized BLASTN algorithms offer substantial speed enhancements for nucleotide sequence analysis.
The new methods provide accurate alignments efficiently, crucial for large genomic datasets.
These advancements facilitate faster discovery in genomics and molecular biology.