Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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...
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...
Fast Fourier Transform01:10

Fast Fourier Transform

The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
Atomic Force Microscopy01:08

Atomic Force Microscopy

Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
The AFM Probe
The probe is regarded as the heart of any AFM setup and comprises the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Knowledge of oxygen therapy among healthcare professionals in non-intubated patients: a cross-sectional study in Somalia.

BMC medical education·2026
Same author

Towards a decentralized future for open-science databases.

Nature genetics·2026
Same author

Rapid adaptive increase of amylase gene copy number in Indigenous Andeans.

Nature communications·2026
Same author

A novel anti-CD20, concabody, enhances immunotherapy efficacy by targeting MPZL1 and augmenting antibody-induced cell death.

Frontiers in oncology·2026
Same author

Interaction of Soil Type and Elevated Temperature Drives the Emergence of Macrophomina phaseolina in Soybean Fields.

The plant pathology journal·2026
Same author

LCPAN: efficient variation graph construction using locally consistent parsing.

Genome biology·2026
Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026
Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026
Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026
Same journal

Correction: TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: May 14, 2026

Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays for High-Throughput Large-Scale Sample Inspection
05:04

Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays for High-Throughput Large-Scale Sample Inspection

Published on: June 13, 2023

Accelerating read mapping with FastHASH.

Hongyi Xin1, Donghyuk Lee, Farhad Hormozdiari

  • 1Depts. of Computer Science and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

BMC Genomics
|February 2, 2013
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) generates massive genomic data. A new algorithm, FastHASH, significantly speeds up read mapping for NGS data analysis while maintaining accuracy and sensitivity.

More Related Videos

A Multimodal Wide-Field Fourier-Transform Raman Microscope
06:48

A Multimodal Wide-Field Fourier-Transform Raman Microscope

Published on: December 30, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
09:08

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Related Experiment Videos

Last Updated: May 14, 2026

Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays for High-Throughput Large-Scale Sample Inspection
05:04

Active Probe Atomic Force Microscopy with Quattro-Parallel Cantilever Arrays for High-Throughput Large-Scale Sample Inspection

Published on: June 13, 2023

A Multimodal Wide-Field Fourier-Transform Raman Microscope
06:48

A Multimodal Wide-Field Fourier-Transform Raman Microscope

Published on: December 30, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
09:08

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) produces vast amounts of genomic data.
  • Efficient computational methods are crucial for analyzing NGS data in medical and genetic applications.
  • Current read mapping algorithms struggle with the scale of NGS data.

Purpose of the Study:

  • To develop a novel algorithm that enhances the performance of seed-and-extend read mapping.
  • To address the computational challenges posed by the massive data volumes in NGS.
  • To improve the speed and efficiency of genomic sequence analysis.

Main Methods:

  • Introduction of the FastHASH algorithm, a generic enhancement for seed-and-extend read mappers.
  • Implementation of two key techniques: Adjacency Filtering and Cheap K-mer Selection.
  • Integration of FastHASH into the mrFAST read mapping program.

Main Results:

  • FastHASH offers significant performance improvements for read mapping algorithms.
  • Observed speedups of up to 19-fold, depending on edit distance cutoffs.
  • Maintained 100% sensitivity and high comprehensiveness of the read mapping process.

Conclusions:

  • FastHASH drastically improves the speed of hash table-based read mapping algorithms.
  • The algorithm is compatible with existing seed-and-extend methods.
  • FastHASH enables faster and more efficient analysis of large-scale genomic data from NGS.