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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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...
Gene Evolution - Fast or Slow?02:05

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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...

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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Interpolated Markov models for eukaryotic gene finding.

S L Salzberg1, M Pertea, A L Delcher

  • 1The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA. salzberg@tigr.org

Genomics
|July 9, 1999
PubMed
Summary

A new gene finding system, GlimmerM, was developed for the malaria parasite Plasmodium falciparum. This tool aids in annotating the Plasmodium falciparum genome, crucial for understanding this pathogen.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Existing gene finders primarily target bacterial and human DNA.
  • Small eukaryotes, like the malaria parasite, often lack specialized gene-finding tools.

Purpose of the Study:

  • To develop a novel gene finding system, GlimmerM, tailored for the Plasmodium falciparum genome.
  • To address the specific needs of gene identification in this important eukaryotic pathogen.

Main Methods:

  • GlimmerM was based on the Glimmer bacterial gene finder due to high gene density in P. falciparum.
  • The system incorporated specialized modules for splice site identification.
  • Training utilized comprehensive available data from the P. falciparum genome.

Main Results:

  • Laboratory validation using RT-PCR confirmed all predicted genes from a small test set.
  • GlimmerM successfully identified genes within the Plasmodium falciparum genome.

Conclusions:

  • GlimmerM is a valuable new tool for facilitating the annotation of the Plasmodium falciparum genome.
  • The system's development is timely given the rapid progress in P. falciparum genome sequencing.