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Related Concept Videos

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...
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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...

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

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Published on: August 15, 2019

A cross-species alignment tool (CAT).

Heng Li1, Liang Guan, Tao Liu

  • 1Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China. lh3@sanger.ac.uk

BMC Bioinformatics
|September 21, 2007
PubMed
Summary

A new algorithm, Cross-species Alignment Tool (CAT), enhances gene annotation by aligning mRNA sequences to genomes. CAT offers superior speed, specificity, and sensitivity compared to existing tools.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Automatic gene annotation relies on ab initio and alignment-based frameworks.
  • Alignment-based methods include intra-species (high specificity/speed) and inter-species (high sensitivity) approaches.

Purpose of the Study:

  • To introduce a novel algorithm, Cross-species Alignment Tool (CAT), for aligning mRNA sequences to mammalian genomes.

Main Methods:

  • CAT is implemented using C scripts.
  • The tool is accessible online for public use.

Main Results:

  • CAT demonstrates superior performance compared to existing alignment tools.
  • Evaluations on mouse-human and zebrafish-human orthologs confirm CAT's effectiveness.

Conclusions:

  • CAT integrates the speed and specificity of intra-species aligners with the sensitivity of inter-species aligners.
  • This makes CAT a powerful tool for cross-species gene annotation.