SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically

Protein and Peptide Letters
Qing ZhanYadong Wang

Abstract

Multiple Sequence Alignment (MSA) is a fundamental task in bioinformatics and is required for many biological analysis tasks. The more accurate the alignments are, the more credible the downstream analyses. Most protein MSA algorithms realign an alignment to refine it by dividing it into two groups horizontally and then realign the two groups. However, this strategy does not consider that different regions of the sequences have different conservation; this property may lead to incorrect residue-residue or residue-gap pairs, which cannot be corrected by this strategy. In this article, our motivation is to develop a novel refinement method based on splitting- splicing vertically. Here, we present a novel refinement method based on splitting-splicing vertically, called SpliVert. For an alignment, we split it vertically into 3 parts, remove the gap characters in the middle, realign the middle part alone, and splice the realigned middle parts with the other two initial pieces to obtain a refined alignment. In the realign procedure of our method, the aligner will only focus on a certain part, ignoring the disturbance of the other parts, which could help fix the incorrect pairs. We tested our refinement strategy for 2 leading MSA tool...Continue Reading

References

Oct 1, 1991·Computer Applications in the Biosciences : CABIOS·M P Berger, P J Munson
Oct 20, 1989·Journal of Molecular Biology·S Subbiah, S C Harrison
Jan 1, 1987·Journal of Molecular Evolution·D F Feng, R F Doolittle
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Jun 1, 1993·Computer Applications in the Biosciences : CABIOS·O Gotoh
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·S RajasekaranJ L Spouge
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Oct 14, 2003·BMC Bioinformatics·G P S RaghavaGeoffrey J Barton
Feb 14, 2004·Bioinformatics·Ivo Van WalleLode Wyns
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jan 14, 2005·Bioinformatics·F ChalmelO Poch
Feb 3, 2005·Genome Research·Chuong B DoSerafim Batzoglou
Jul 27, 2005·Nucleic Acids Research·Julie D ThompsonOlivier Poch
Sep 7, 2006·Bioinformatics·Usman Roshan, Dennis R Livesay
Jan 6, 2010·Nucleic Acids Research·Robert C Edgar
Apr 24, 2010·Nucleic Acids Research·Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon
May 18, 2010·Algorithms for Molecular Biology : AMB·Gordon BlackshieldsDesmond G Higgins
Jul 31, 2010·Molecular Biology and Evolution·Zheng ZhangPeiji Gao
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 12, 2013·Briefings in Bioinformatics·Quan ZouKe Chen
Apr 11, 2015·BMC Bioinformatics·Qing ZhanHing-Fung Ting
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yongtao YeHing-Fung Ting
Nov 29, 2015·Briefings in Bioinformatics·Maria ChatzouCedric Notredame
Dec 22, 2016·International Journal of Molecular Sciences·Leyi Wei, Quan Zou
Jun 24, 2017·Nucleic Acids Research·Laura E RitcheyPhilip C Bevilacqua
Oct 3, 2017·Briefings in Bioinformatics·Liang ChengMeng Zhou
Nov 9, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wenhe SuShaoliang Peng
Jan 4, 2018·BMC Systems Biology·Quan ZouZhanshan Sam Ma
May 18, 2018·Systematic Biology·Haim AshkenazyTal Pupko
Oct 12, 2018·Current Gene Therapy·Liang Cheng, Yang Hu
Nov 1, 2018·Nucleic Acids Research·Liang ChengQinghua Jiang

❮ Previous
Next ❯

Citations

Mar 25, 2020·Protein and Peptide Letters·Hao Lin
Aug 24, 2021·Computational Biology and Chemistry·Anderson Rici AmorimLiria Matsumoto Sato

❮ 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.

© 2021 Meta ULC. All rights reserved