A Modified Multiple Alignment Fast Fourier Transform with Higher Efficiency

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Weihua ZhengHing Cheung So

Abstract

Multiple sequence alignment (MSA) is the most common task in bioinformatics. Multiple alignment fast Fourier transform (MAFFT) is the fastest MSA program among those the accuracy of the resulting alignments can be comparable with the most accurate MSA programs. In this paper, we modify the correlation computation scheme of the MAFFT for further efficiency improvement in three aspects. First, novel complex number based amino acid and nucleotide expressions are utilized in the modified correlation. Second, linear convolution with a limitation is proposed for computing the correlation of amino acid and nucleotide sequences. Third, we devise a fast Fourier transform (FFT) algorithm for computing linear convolution. The FFT algorithm is based on conjugate pair split-radix FFT and does not require the permutation of order, and it is new as only real parts of the final outputs are required. Simulation results show that the speed of the modified scheme is 107.58 to 365.74 percent faster than that of the original MAFFT for one execution of the function Falign() of MAFFT, indicating its faster realization.

References

Mar 15, 1979·Journal of Molecular Evolution·T MiyataT Yasunaga
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Jan 1, 1984·Journal of Molecular Evolution·T H Jukes, M Kimura
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Apr 15, 1996·Nucleic Acids Research·C Notredame, D G Higgins
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·L Wang, T Jiang
Jun 2, 1998·Bioinformatics·J StoyeF Meyer
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Mar 4, 2003·Bioinformatics·Susana Vinga, Jonas Almeida
Jul 23, 2003·Bioinformatics·Robert C Edgar, Kimmen Sjölander
Jul 27, 2005·Proteins·Julie D ThompsonOlivier Poch
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
Jul 12, 2008·BMC Bioinformatics·David J RussellKhalid Sayood
May 30, 2009·PLoS Computational Biology·Robert K BradleyLior Pachter
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Dec 18, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ken D Nguyen, Yi Pan

❮ Previous
Next ❯

Citations

May 1, 2020·Sensors·Jifang RongYuzhe Xiao

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.