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06:38
Pattern-based Search of Epigenomic Data Using GeNemo
Published on: October 8, 2017
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
Thierry Schuepbach1, Marco Pagni, Alan Bridge
1Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne, Switzerland.
Bioinformatics (Oxford, England)
|March 19, 2013
Summary
The PROSITE resource accelerates protein domain detection. A new, optimized search tool (pfsearchV3) significantly speeds up database searches, making genome annotation more efficient.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- The PROSITE database offers valuable protein domain signatures for functional annotation.
- Current PROSITE search methods are time-consuming, limiting their use in large-scale genome and metagenome annotation.
Purpose of the Study:
- To improve the efficiency of the PROSITE search tool, pfsearch.
- To address the computational bottleneck in protein domain detection for large-scale sequence analysis.
Main Methods:
- Developed an optimized implementation of the pfsearch tool, named pfsearchV3.
- Integrated a novel heuristic to enhance search speed and accuracy.
- Benchmarked performance on modern multi-core processors.
Main Results:
- The new pfsearchV3 is two orders of magnitude faster than the original algorithm.
- The optimized tool significantly reduces the time required for protein sequence database searches.
- The implementation is available in C and supported on Linux.
Conclusions:
- pfsearchV3 offers a substantial speed improvement for PROSITE searches.
- This advancement facilitates the application of PROSITE in genome and metagenome annotation pipelines.
- The optimized tool enhances the utility of the PROSITE resource for protein functional analysis.
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