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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Transcription Elongation Factors02:35

Transcription Elongation Factors

Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA into a...

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Related Experiment Video

Updated: May 21, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

Yuki Naito1, Hidemasa Bono

  • 1Database Center for Life Science, Research Organization of Information and Systems, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

Nucleic Acids Research
|May 30, 2012
PubMed
Summary
This summary is machine-generated.

GGRNA is a fast, free search engine for genes and transcripts. It allows searching by various keywords, including short nucleotide or amino acid sequences, enhancing biological data retrieval.

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Related Experiment Videos

Last Updated: May 21, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Efficient retrieval of gene and transcript information is crucial for biological research.
  • Existing search tools often have limitations in handling diverse query types and short sequences.

Purpose of the Study:

  • To introduce GGRNA, an ultrafast, Google-like search engine for genes and transcripts.
  • To provide a versatile platform for searching biological data using various keywords and sequence inputs.

Main Methods:

  • Developed a web server accepting gene names, IDs, descriptions, annotations, and nucleotide/amino acid sequences.
  • Implemented a search functionality supporting up to three mismatches and degenerate nucleotide codes.
  • Integrated Gene Ontology, Enzyme Commission numbers, and microarray probe data.

Main Results:

  • GGRNA provides ultrafast search results for genes and transcripts within seconds.
  • The engine efficiently handles short sequences (10 nt or 4 amino acids) and complex queries.
  • Incorporates diverse data types, including functional annotations and probe sequences, for comprehensive searching.

Conclusions:

  • GGRNA offers a simple, powerful, and free interface for gene and transcript discovery.
  • Its speed and flexibility significantly enhance usability for researchers in various biological fields.
  • The tool supports diverse search strategies, improving biological data accessibility.