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TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy
Basharat Bhat1, Nazir A Ganai2, Syed Mudasir Andrabi2
1Department of Life Science, Shiv Nadar University, Greater Noida, UP, 201314, India.
Scientific Reports
|October 4, 2017
Summary
TM-Aligner is a novel tool for aligning transmembrane protein sequences, offering improved accuracy and speed. This new method addresses computational demands, outperforming existing tools in benchmarking tests.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Membrane proteins are crucial cellular components, representing about 30% of proteins.
- Developing accurate alignment tools for transmembrane proteins is challenging due to limited structural data.
- Homology modeling tools offer moderate accuracy but are computationally intensive for large datasets.
Purpose of the Study:
- To introduce TM-Aligner, a new, efficient tool for transmembrane protein sequence alignment.
- To enhance the speed and accuracy of multiple sequence alignment for transmembrane proteins.
- To provide a freely accessible resource for the scientific community.
Main Methods:
- TM-Aligner utilizes the Wu-Manber and dynamic string matching algorithms.
- Performance was benchmarked against established tools like PROMALS, MAFFT, and ClustalW.
- Validation employed three distinct reference datasets: BaliBASE3.0, Pfam, and GPCRDB.
Main Results:
- TM-Aligner demonstrates significantly improved accuracy and speed in multiple sequence alignment.
- Benchmarking confirmed TM-Aligner's superior performance compared to existing popular alignment tools.
- The tool achieved the least turnaround time among tested methods.
Conclusions:
- TM-Aligner represents an advanced method for transmembrane protein sequence alignment.
- Its efficiency and accuracy make it a valuable tool for large-scale sequence analysis.
- TM-Aligner is available online, facilitating broader research applications.
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