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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
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.
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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.
Nucleic Acid Structure01:25

Nucleic Acid Structure

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DNA Structure
DNA has a double-helix structure. The...

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Updated: May 10, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Alns: a new searchable and filterable sequence alignment format.

Ross K K Leung1, Stephen K W Tsui

  • 1Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong. ross@cuhk.edu.hk

International Journal of Data Mining and Bioinformatics
|June 20, 2013
PubMed
Summary
This summary is machine-generated.

A new alignment format, alns, simplifies associating genetic changes with biological data. This format enhances knowledge discovery for researchers working with large datasets of RNA, DNA, and protein sequences.

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Last Updated: May 10, 2026

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Published on: February 5, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Nucleotides and amino acids are fundamental units of nucleic acids and proteins.
  • Current alignment formats, like those from BLAST, are cumbersome for managing large datasets.
  • Efficiently linking genetic variations to biological information is crucial for research.

Purpose of the Study:

  • Introduce a novel alignment format, alns, for improved data management.
  • Facilitate the association of genetic changes with diverse biological information.
  • Enhance knowledge discovery in molecular biology and related fields.

Main Methods:

  • Development of the 'alns' alignment format.
  • Utilizing simple spreadsheet functions for data association.
  • Focus on handling large-scale, highly conserved sequence alignments.

Main Results:

  • The 'alns' format enables rapid searching, filtering, and storage of alignment data.
  • Facilitates easy correlation of genetic alterations with phenotypes, diseases, and taxonomy.
  • Demonstrates utility for biologists across various disciplines.

Conclusions:

  • The 'alns' format offers a user-friendly solution for managing complex biological sequence data.
  • Significantly improves the efficiency of linking genetic information to broader biological contexts.
  • Supports advanced knowledge discovery by simplifying data integration and analysis.