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Updated: Jul 14, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment
Maricel G Kann1, Sergey L Sheetlin, Yonil Park
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.
Nucleic Acids Research
|June 29, 2007
Summary
Automated gene function annotation requires accurate domain alignment. GLOBAL, a new tool using Hidden Markov Models (HMMs), offers accurate E-values and heuristic acceleration for efficient, precise protein domain identification.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Automated gene function annotation is crucial for analyzing complete genome sequences.
- Protein domains are fundamental units of protein function and evolution, necessitating accurate domain identification.
- Current high-throughput annotation often relies on local alignment, which may not identify complete domains effectively.
Purpose of the Study:
- To address limitations in semi-global alignment for protein domain identification.
- To introduce GLOBAL, a novel tool for semi-global alignment using Hidden Markov Models (HMMs).
- To evaluate GLOBAL's performance against existing alignment tools.
Main Methods:
- Development of the GLOBAL tool for semi-global HMM alignment.
- Comparison of GLOBAL with HMMer (semi-global HMM) and local alignment tools.
- Performance evaluation based on protein structure as a standard of truth for complete domain identification.
Main Results:
- GLOBAL provides accurate E-values and heuristic acceleration for high-throughput applications.
- GLOBAL and HMMer demonstrated comparable performance in identifying complete domains.
- Both GLOBAL and HMMer significantly outperformed local alignment tools in retrieving complete protein domains.
Conclusions:
- GLOBAL overcomes limitations of previous semi-global HMMs, offering efficiency and accuracy.
- GLOBAL provides superior performance for complete protein domain searching compared to local alignment methods.
- The study highlights the advantage of semi-global HMM alignment for accurate gene function annotation.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.