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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...
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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 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...

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Updated: Jun 22, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

The Sequence Alignment/Map format and SAMtools.

Heng Li1, Bob Handsaker, Alec Wysoker

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.

Bioinformatics (Oxford, England)
|June 10, 2009
PubMed
Summary
This summary is machine-generated.

The Sequence Alignment/Map (SAM) format stores read alignments for various sequencing platforms. SAMtools provides essential utilities for processing these alignments, including indexing and variant calling.

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The ITS2 Database
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Area of Science:

  • Bioinformatics
  • Genomics

Background:

  • The Sequence Alignment/Map (SAM) format is a widely adopted standard for storing sequence read alignments.
  • It supports diverse sequencing platforms and read lengths, accommodating data from large-scale projects like the 1000 Genomes Project.

Purpose of the Study:

  • To introduce the Sequence Alignment/Map (SAM) format and its associated utilities (SAMtools).
  • To highlight the flexibility, compactness, and efficiency of the SAM format for genomic data storage and retrieval.

Main Methods:

  • Description of the SAM format's features and capabilities.
  • Overview of SAMtools functionalities for post-processing SAM-formatted alignments.

Main Results:

  • The SAM format efficiently stores alignments from various sequencing technologies.
  • SAMtools offers crucial tools for alignment manipulation, including indexing and variant detection.

Conclusions:

  • The SAM format is a versatile and efficient standard for genomic read alignments.
  • SAMtools provides a comprehensive toolkit for post-processing SAM alignments, facilitating downstream genomic analyses.