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Related Concept Videos

Sequences01:29

Sequences

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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Maxam-Gilbert Sequencing01:05

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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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Multi-species Conserved Sequences02:51

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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.
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Sanger Sequencing01:57

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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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RNA-seq03:21

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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. 
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Next-generation Sequencing03:00

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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.
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Novel Sequence Discovery by Subtractive Genomics
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Seqotron: a user-friendly sequence editor for Mac OS X.

Mathieu Fourment1,2, Edward C Holmes3

  • 1The ithree institute, University of Technology Sydney, Sydney, Australia. mathieu.fourment@uts.edu.au.

BMC Research Notes
|February 19, 2016
PubMed
Summary
This summary is machine-generated.

Seqotron is a new open-source sequence editor for Mac OS X. It simplifies manual editing and alignment of complex biological sequences, aiding bioinformatics and evolutionary analyses.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Accurate multiple sequence alignment is crucial for bioinformatics and molecular evolutionary studies.
  • Existing alignment programs often require manual adjustments for optimal quality.
  • Intuitive tools for editing sequence alignments are limited.

Purpose of the Study:

  • To introduce Seqotron, a novel sequence editor designed for user-friendly manipulation of biological sequences.
  • To provide researchers with a tool that facilitates both automated and manual sequence alignment.
  • To offer integrated functionalities for phylogenetic analysis.

Main Methods:

  • Seqotron supports a wide range of sequence file formats for input and output.
  • Users can perform sequence alignment and manual editing using intuitive mouse and keyboard controls.
  • The software includes integrated modules for estimating phylogenetic trees and distance matrices.

Main Results:

  • Seqotron enables efficient alignment and manual editing of biological sequences.
  • The tool supports various sequence formats, enhancing data compatibility.
  • Phylogenetic trees and distance matrices can be readily generated within the program.

Conclusions:

  • Seqotron offers a valuable solution for researchers working with complex sequence data.
  • The open-source nature and Mac OS X compatibility make Seqotron accessible.
  • This tool can significantly benefit bioinformatics and molecular evolutionary research.