Related Experiment Video
Updated: Apr 14, 2026
09:40
Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
9.3K
aTRAM - automated target restricted assembly method: a fast method for assembling loci across divergent taxa from
Julie M Allen1, Daisie I Huang2, Quentin C Cronk3
1Illinois Natural History Survey, University of Illinois, Champaign, IL, 61820, USA. juliema@illinois.edu.
BMC Bioinformatics
|April 19, 2015
Summary
Automated Target Restricted Assembly Method (aTRAM) software rapidly assembles genes from diverse species using a single data library. This tool significantly speeds up gene assembly for phylogenomic studies, even without a reference genome.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Gene assembly from next-generation sequencing data is computationally intensive and time-consuming, especially for species lacking a reference genome.
- De novo genome assembly requires multiple genomic libraries and can take days on powerful computers.
- Existing methods present challenges for assembling genes from distantly related taxa.
Purpose of the Study:
- To introduce a novel software, automated Target Restricted Assembly Method (aTRAM), for rapid gene assembly.
- To address the computational difficulties and time constraints associated with gene assembly, particularly for taxa without closely related reference genomes.
- To enable efficient gene assembly from a single library of paired-end reads.
Main Methods:
- aTRAM utilizes a reference sequence and BLAST for targeted gene assembly.
- The software employs an iterative approach to locally assemble genes of interest.
- It processes a single library of paired-end reads for gene assembly.
Main Results:
- aTRAM demonstrated rapid gene assembly across distantly related taxa, completing assembly in under one minute per gene in comparative tests.
- The software successfully assembled over 1,000 genes from six taxa with sequence divergence ranging from 25 to 110 million years.
- Gene recovery rates ranged from 97% to 99% for the tested divergent taxa.
Conclusions:
- aTRAM efficiently assembles genes from distantly related taxa, eliminating the need for complete draft genome assembly.
- The targeted approach allows for rapid locus assembly, often within minutes.
- This software is valuable for phylogenomic projects with broad taxonomic scope and other genomic applications.
Related Concept Videos
03:36Genome Annotation and Assembly
22.2K
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.
22.2K
01:29Modern Molecular Taxonomy
861
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
861
03:00Next-generation Sequencing
101.9K
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....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
101.9K
02:54Evolutionary Relationships through Genome Comparisons
7.3K
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...
7.3K