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Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

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...
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...

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Related Experiment Video

Updated: Jun 5, 2026

Introductory Analysis and Validation of CUT&#38;RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.

Guorong Xu1, Nan Deng, Zhiyu Zhao

  • 1Department of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA. dzhu@cs.uno.edu.

Source Code for Biology and Medicine
|January 15, 2011
PubMed
Summary

SAMMate is a new GUI tool that simplifies accessing Next Generation Sequencing (NGS) alignment data in SAM/BAM files for biomedical researchers. It automates analysis and facilitates downstream processing of DNA-seq and RNA-seq data.

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Last Updated: Jun 5, 2026

Introductory Analysis and Validation of CUT&#38;RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next Generation Sequencing (NGS) generates large volumes of short DNA/RNA reads.
  • Short read alignment to a reference genome is crucial for NGS data analysis.
  • Accessing alignment data in standard Sequence Alignment/Map (SAM) or Binary SAM (BAM) formats remains challenging for researchers.

Purpose of the Study:

  • To develop a user-friendly Graphical User Interface (GUI) software tool named SAMMate.
  • To enable biomedical researchers to easily access and analyze SAM/BAM alignment files.
  • To streamline downstream analysis of NGS data.

Main Methods:

  • Developed SAMMate, a GUI software tool for processing SAM/BAM files.
  • Ensured compatibility with single-end and paired-end sequencing technologies.
  • Automated standard DNA-seq and RNA-seq analysis procedures.
  • Enabled calculation of genomic interval coverage using custom annotation files.
  • Facilitated gene expression abundance scoring for RNA-seq data.
  • Generated whole-genome signal maps at base-wise resolution.

Main Results:

  • SAMMate provides quick processing of SAM/BAM files for biomedical researchers.
  • Accurate calculation of short read coverage and gene expression abundance is achieved.
  • Whole-genome signal maps enable diverse bioinformatics problem-solving.
  • Export functionality includes wiggle files for visualization and alignment statistics reports.
  • Case studies demonstrate biological impact, including miRNA target prediction.

Conclusions:

  • SAMMate offers intuitive access to critical alignment information in SAM/BAM files.
  • The software significantly facilitates downstream analysis of NGS data.
  • Source code and executable are freely available, promoting widespread adoption and further development.