Related Experiment Video
Updated: May 26, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
Michael Remmert1, Andreas Biegert, Andreas Hauser
1Gene Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians Universität München, Munich, Germany.
Nature Methods
|December 27, 2011
Summary
HHblits is a new tool for protein sequence analysis. It uses profile hidden Markov models (HMMs) for faster, more sensitive, and accurate protein function and structure prediction.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Protein function and structure prediction are vital for biological research.
- Accurate sequence alignments are crucial for these predictions.
- Existing tools like PSI-BLAST have limitations in speed and sensitivity.
Purpose of the Study:
- To introduce HHblits, a novel tool for sequence-based protein analysis.
- To improve the sensitivity and accuracy of sequence alignments.
- To provide a faster alternative to existing sequence search tools.
Main Methods:
- Utilizing profile hidden Markov models (HMMs) for both query and database sequences.
- Implementing a discretized-profile prefilter for accelerated searching.
- Developing an iterative search strategy for enhanced accuracy.
Main Results:
- HHblits demonstrates significantly higher sensitivity (50-100%) compared to PSI-BLAST.
- HHblits generates more accurate sequence alignments.
- The tool offers a considerable speed improvement over PSI-BLAST.
Conclusions:
- HHblits represents a significant advancement in sequence-based protein function and structure prediction.
- The tool's speed, sensitivity, and accuracy make it valuable for biological research.
- HHblits is an open-source, general-purpose tool readily available to the scientific community.
Related Concept Videos
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:33Peptide Identification Using Tandem Mass Spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...