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Related Concept Videos

Trihybrid Crosses02:27

Trihybrid Crosses

Trihybrid Crosses
Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
The F1 generation plants of a trihybrid cross are heterozygous for all three traits and produce eight gametes. Upon self-fertilization, these gametes have an equal chance to...
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In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
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Overview
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...

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In Situ Hybridization for the Precise Localization of Transcripts in Plants
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A hybrid method for the exact planted (l, d) motif finding problem and its parallelization.

Mostafa M Abbas1, Mohamed Abouelhoda, Hazem M Bahig

  • 1Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt. mabbas@su.edu.eg

BMC Bioinformatics
|January 4, 2013
PubMed
Summary

This study introduces a hybrid method to accelerate the exact motif finding problem, improving computational efficiency for discovering DNA motifs. The new approach offers significant speed-ups and enables solving larger motif instances.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The (l, d) motif problem seeks an l-length motif M in t DNA sequences, allowing up to d mismatches per sequence.
  • Existing exact algorithms for motif finding are computationally intensive and limited to small motif lengths (l) and mismatch counts (d).

Purpose of the Study:

  • To develop an efficient hybrid method that enhances the performance of exact algorithms for the motif finding problem.
  • To enable the discovery of longer motifs and solve more challenging instances of the (l, d) motif problem.

Main Methods:

  • A two-step hybrid approach: 1. Identify candidate motifs from a subset of sequences (q). 2. Search for these candidates in the remaining sequences.
  • Integration of existing state-of-the-art algorithms to optimize runtime.
  • Determination of the optimal subset size (q) for maximum efficiency.
  • Development of a parallel version for shared memory architectures.

Main Results:

  • Achieved approximately 24% speed-up compared to the best existing algorithm.
  • Demonstrated linear scalability of the parallel version with the number of processors.
  • Successfully solved a challenging (21, 8) motif instance in 20.42 hours using 8 processors, compared to 6.68 days for the serial version.

Conclusions:

  • The proposed hybrid method significantly accelerates the exact motif problem solution.
  • The method is generic and adaptable to new, faster algorithms.
  • Expectation of facilitating the discovery of longer motifs.
  • Developed software is freely available for academic research.