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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Related Experiment Video

Updated: Jun 1, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

HMMER web server: interactive sequence similarity searching.

Robert D Finn1, Jody Clements, Sean R Eddy

  • 1HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA. finnr@janelia.hhmi.org

Nucleic Acids Research
|May 20, 2011
PubMed
Summary
This summary is machine-generated.

The HMMER web server provides fast protein sequence similarity searches using profile hidden Markov models (profile HMMs). This accessible tool significantly speeds up analysis, making complex bioinformatics tasks easier for researchers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • HMMER is a probabilistic software suite for protein sequence similarity searches.
  • Previous HMMER versions were computationally intensive command-line tools, limiting accessibility.
  • HMMER3 offers a 100-fold speed improvement over prior versions.

Purpose of the Study:

  • To introduce an efficient web server for profile hidden Markov model (profile HMM) searches.
  • To provide rapid protein sequence database searching capabilities.
  • To enhance accessibility and usability of HMMER for a wider range of users.

Main Methods:

  • Development and implementation of the HMMER web server (http://hmmer.janelia.org).
  • Integration of profile HMM search methods for single sequences, multiple sequence alignments, and against databases like Pfam.
  • Provision of RESTful web services for integration into scripted workflows.
  • Design for batch uploading of multiple queries and catering to various user expertise levels.

Main Results:

  • Protein database searches on the HMMER web server typically complete within seconds.
  • The server supports diverse search strategies, including sequence-to-database and sequence-to-Pfam.
  • Graphical summaries enhance the intuitive appraisal of search results.

Conclusions:

  • The HMMER web server democratizes access to powerful protein sequence analysis tools.
  • Significant speed gains in HMMER3 enable near real-time bioinformatics analyses.
  • The server's design facilitates both interactive use and programmatic integration.