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Related Concept Videos

Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm.

Ivan Antonov1, Mark Borodovsky

  • 1Division of Computational Science and Engineering, Georgia Institute of Technology, 801 Atlantic Drive, Atlanta, Georgia 30332-0280, USA. ivan.antonov@gatech.edu

Journal of Bioinformatics and Computational Biology
|June 18, 2010
PubMed
Summary
This summary is machine-generated.

GeneTack is a new program for ab initio frameshift detection in nucleotide sequences. It accurately distinguishes true genes from frameshifted ones, outperforming existing methods.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Frameshifts in protein-coding sequences can lead to spurious gene predictions.
  • Distinguishing true overlapping genes from frameshift-induced ORFs is a significant challenge in gene finding.

Purpose of the Study:

  • To introduce GeneTack, a novel program for accurate ab initio frameshift detection.
  • To evaluate GeneTack's performance against existing frameshift detection tools.

Main Methods:

  • GeneTack utilizes a hidden Markov model (HMM) and the Viterbi algorithm.
  • The program models genomic sequences with potentially frameshifted protein-coding regions.
  • Performance was assessed on 17 prokaryotic genomes with simulated frameshifts.

Main Results:

  • GeneTack demonstrated significantly higher average frameshift prediction accuracy compared to FrameD and FSFind.
  • GeneTack's accuracy favorably compared with FSFind-BLAST, despite not using external evidence.
  • The program effectively identifies spurious gene predictions caused by frameshifts.

Conclusions:

  • GeneTack offers a robust and accurate solution for ab initio frameshift detection.
  • The program improves the reliability of gene prediction in prokaryotic genomes.
  • GeneTack is freely available for research use.