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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

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...
Genome Annotation and Assembly03:36

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.
Next-generation Sequencing03:00

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.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Multi-species Conserved Sequences02:51

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...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Related Experiment Video

Updated: May 26, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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User Guided Selection and Alignment of Sequence Data by GeneMatrix.

Simon J Goodman1, Ian M Carr2

  • 1School of Biology, Faculty of Biological Science, University of Leeds, Leeds, LS2 9JT, UK.

Journal of Molecular Evolution
|May 25, 2026
PubMed
Summary
This summary is machine-generated.

GeneMatrix simplifies retrieving and aligning DNA and protein sequences from large databases like GenBank. This tool aids researchers in extracting, filtering, and aggregating genetic data for biological analysis.

Keywords:
Multiple sequence alignmentsPhylogeneticsSoftware

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Last Updated: May 26, 2026

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Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Multiple sequence alignment is crucial for identifying conserved regions in DNA and protein sequences, aiding in pathogenicity scoring, functional domain detection, and evolutionary mapping.
  • High-throughput sequencing has generated vast amounts of data, making data retrieval and filtering from repositories like GenBank a significant bottleneck.
  • Accessing and processing data for less common sequences from GenBank can be challenging for researchers.

Purpose of the Study:

  • To develop a novel application, GeneMatrix, to streamline the process of extracting, filtering, aggregating, and aligning DNA and protein sequences.
  • To address the challenges associated with data retrieval and processing for diverse and less common sequences from GenBank.
  • To facilitate biological research by simplifying access to sequence data for alignment-based analyses.

Main Methods:

  • Development of the GeneMatrix application for sequence data management.
  • Implementation of functionalities for extraction, filtering, and aggregation of sequences from GenBank-formatted files.
  • Support for aligning DNA and protein sequences from single genes or entire genomes (e.g., viruses, mitochondria).

Main Results:

  • GeneMatrix provides an efficient solution for handling large-scale sequence data retrieval and preparation.
  • The application simplifies the process of obtaining and aligning sequences, particularly for less common or specialized datasets.
  • Facilitates downstream analyses such as identifying conserved regions, functional domains, and evolutionary relationships.

Conclusions:

  • GeneMatrix effectively addresses the challenges in data retrieval and alignment posed by the exponential growth of sequence databases.
  • The application enhances the efficiency of bioinformatics workflows, enabling researchers to focus on biological interpretation rather than data wrangling.
  • GeneMatrix is a valuable tool for researchers across various biological fields requiring sequence alignment for diverse applications.