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

Accelerators01:17

Accelerators

Accelerators in concrete serve as admixtures to speed up the hardening process, enabling the concrete to achieve early strength faster. Although accelerators do not necessarily impact the time it takes concrete to set, they reduce this time in practice. A common accelerator is calcium chloride, which is particularly useful for hastening early strength development in cold weather or for rapid repair jobs that require quick heat generation after mixing.
The effectiveness of calcium chloride can...
Instantaneous Acceleration01:16

Instantaneous Acceleration

Acceleration is in the direction of the change in velocity, but it is not always in the direction of motion. When an object slows down, its acceleration is opposite to the direction of its motion. Although commonly referred to as deceleration, this causes confusion in our analysis as deceleration is not a vector, and does not point to a specific direction with respect to a coordinate system. Therefore, the term deceleration is not used. For example, when a subway train slows down, it...
Average Acceleration01:30

Average Acceleration

The importance of understanding acceleration spans our day-to-day experiences, as well as the vast reaches of outer space and the tiny world of subatomic physics. In everyday conversation, to accelerate means to speed up. For instance, we are familiar with the acceleration of our car; the harder we apply our foot to the gas pedal, the faster we accelerate. The greater the acceleration, the greater the change in velocity over a given time. Acceleration is widely seen in experimental physics. In...
Profile Leveling and Cross Sections01:26

Profile Leveling and Cross Sections

Profile leveling and cross-sections are surveying methods used to determine and document terrain elevations for infrastructure projects such as highways, railroads, canals, and pipelines. These methods provide data for earthwork planning and alignment of proposed routes.  Profile leveling involves measuring elevations along a fixed line to create a vertical terrain profile. A surveyor sets up a leveling instrument at the benchmark (BM) and records a backsight (BS) to determine the instrument's...
Relative Motion Analysis - Acceleration01:10

Relative Motion Analysis - Acceleration

A slider-crank mechanism converts rotational motion from the crank into linear motion of the slider or vice versa. This mechanism consists of three main parts: the crank, the connecting rod, and the slider. The movement of the slider-crank is an example of general plane motion as the fluctuating angle between the crank and the connecting rod. Consider a segment AB where point A is at the end of the slider and point B is on the diametrically opposite end to point A, on a crack. The variance in...
Acceleration Vectors01:30

Acceleration Vectors

In everyday conversation, accelerating means speeding up. Acceleration is a vector in the same direction as the change in velocity, Δv, therefore the greater the acceleration, the greater the change in velocity over a given time. Since velocity is a vector, it can change in magnitude, direction, or both. Thus acceleration is a change in speed or direction, or both. For example, if a runner traveling at 10 km/h due east slows to a stop, reverses direction, and continues their run at 10 km/h due...

You might also read

Related Articles

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

Sort by
Same author

HMMER web server: 2026 update.

Nucleic acids research·2026
Same author

Induction of menstruation in mice reveals the regulation of menstrual shedding.

bioRxiv : the preprint server for biology·2025
Same author

Presence of group II introns in phage genomes.

Nucleic acids research·2025
Same author

Prevalence of Group II Introns in Phage Genomes.

bioRxiv : the preprint server for biology·2025
Same author

Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice.

eLife·2025
Same author

Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice.

bioRxiv : the preprint server for biology·2024
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: May 28, 2026

Short Session High Intensity Interval Training and Treadmill Assessment in Aged Mice
09:19

Short Session High Intensity Interval Training and Treadmill Assessment in Aged Mice

Published on: February 2, 2019

Accelerated Profile HMM Searches.

Sean R Eddy1

  • 1HHMI Janelia Farm Research Campus, Ashburn, Virginia, United States of America. eddys@janelia.hhmi.org

Plos Computational Biology
|November 1, 2011
PubMed
Summary
This summary is machine-generated.

Profile hidden Markov models (profile HMMs) accelerate sequence database searches. The new HMMER3 software uses multiple segment Viterbi (MSV) and sparse rescaling for faster, sensitive protein homology searches.

More Related Videos

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)
17:12

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

Published on: December 20, 2010

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
09:04

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

Related Experiment Videos

Last Updated: May 28, 2026

Short Session High Intensity Interval Training and Treadmill Assessment in Aged Mice
09:19

Short Session High Intensity Interval Training and Treadmill Assessment in Aged Mice

Published on: February 2, 2019

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)
17:12

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

Published on: December 20, 2010

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
09:04

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Sequence Analysis

Background:

  • Profile hidden Markov models (profile HMMs) are crucial for sequence database homology searches.
  • Existing profile HMM software implementations are computationally expensive, limiting practical applications.

Purpose of the Study:

  • To develop accelerated methods for profile HMM-based sequence database homology searches.
  • To improve the speed and efficiency of profile HMM software without sacrificing sensitivity.

Main Methods:

  • Introduction of the multiple segment Viterbi (MSV) algorithm for rapid ungapped local alignment segment scoring.
  • Implementation of a "sparse rescaling" method to accelerate standard profile HMM Forward/Backward algorithms by 20-fold.
  • Assembly of MSV and sparse rescaling into a pipeline for efficient homology searching, implemented in HMMER3.

Main Results:

  • The MSV algorithm provides scores with a statistical distribution suitable for significance evaluation, acting as an effective heuristic filter.
  • The accelerated pipeline in HMMER3 demonstrates negligible loss in sensitivity compared to unaccelerated profile HMM searches.
  • HMMER3 achieves 100- to 1000-fold speed improvement over HMMER2 and matches the speed of BLAST for protein searches.

Conclusions:

  • The MSV algorithm and sparse rescaling offer significant computational speedups for profile HMM searches.
  • HMMER3 provides a highly sensitive and efficient tool for large-scale sequence database homology searching.
  • The developed methods make profile HMMs more practical for extensive biological sequence analysis.