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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
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Sircah: a tool for the detection and visualization of alternative transcripts.

Eoghan D Harrington1, Peer Bork

  • 1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Bioinformatics (Oxford, England)
|July 19, 2008
PubMed
Summary

Sircah is a flexible bioinformatics tool that detects, analyzes, and visualizes alternative transcription events from gene models or alignments. It aids in understanding complex transcript variations for publication-quality results.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Alternative transcription is crucial for gene expression complexity.
  • Detecting and analyzing alternative transcripts aids in understanding gene regulation.

Purpose of the Study:

  • To present Sircah, a versatile tool for detecting, analyzing, and visualizing alternative transcription events.
  • To provide a comprehensive database of various alternative transcription events.

Main Methods:

  • Input gene models or spliced alignments.
  • Database creation for alternative transcription events (initiation, polyadenylation, splicing, exon skipping, intron retention).
  • Visualization of results for publication-quality images.

Main Results:

  • Sircah successfully detects and categorizes multiple alternative transcription events.
  • The tool generates a structured database of these events.
  • Flexible visualization options are provided for analysis and presentation.

Conclusions:

  • Sircah offers a flexible and comprehensive solution for alternative transcript analysis.
  • The tool facilitates the visualization of complex transcriptomic data.
  • Sircah supports the creation of publication-ready figures for research dissemination.