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An Integrated Approach for Microprotein Identification and Sequence Analysis
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The HMMER Web Server for Protein Sequence Similarity Search.
Ananth Prakash1, Matt Jeffryes1, Alex Bateman1
1European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
Current Protocols in Bioinformatics
|December 9, 2017
Summary
This study details using the HMMER web server for fast and sensitive protein sequence similarity searches. It explains protocols for identifying homologous proteins and functional annotations using profile hidden Markov models (HMMs).
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Protein sequence similarity searches are crucial for identifying evolutionary relationships.
- Existing methods require fast and sensitive algorithms for accurate homolog detection.
Purpose of the Study:
- To describe protocols for utilizing the HMMER web server.
- To enable efficient protein homolog searching and functional annotation.
Main Methods:
- Utilizing the HMMER software (v3.1) which employs profile hidden Markov models (HMMs).
- Leveraging sophisticated acceleration heuristics and computational optimizations.
- Employing the HMMER web server to link algorithms to biological databases.
Main Results:
- The HMMER web server facilitates homology searches and functional annotation.
- Protocols cover various input formats and user-defined parameters for HMMER analysis.
- The software enables fast and sensitive sequence similarity searches.
Conclusions:
- The HMMER web server provides a user-friendly platform for advanced protein sequence analysis.
- Effective utilization of HMMER aids in understanding protein evolution and function.
- The described protocols enhance the accessibility of powerful bioinformatics tools.
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