A comparative analysis of multiple sequence alignments for biological data

Manzoor, Umar; Shahid, Sarosh; Zafar, Bassam

doi:10.3233/bme-151479

Cited by 2 publications

(3 citation statements)

References 18 publications

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“…It is one of the most broadly used sequence alignment programs to date (Bawono et al, ). In fact, recent studies consistently rank MAFFT as one of the top multiple sequence alignment methods in terms of accuracy, speed, and consistency, in comparison to other methods such as T‐Coffee, ClustalW, ProbCons, and Dialign (Chang, Di Tommaso, & Notredame, ; Durand, Hazelhurst, & Coetzer, ; Manzoor, Shahid, & Zafar, ; Nuin, Wang, & Tillier, ; Pais, Ruy, Oliveira, & Coimbra, ; Thompson, Linard, Lecompte, & Poch, ; Wang et al, ; J. Yang & Warnow, ). Coding sequence alignments were subsequently generated by converting amino acid alignments to coding sequence alignments using the PAL2NAL tool (Suyama, Torrents, & Bork, ; http://www.bork.embl.de/pal2nal/).…”

Section: Methodsmentioning

confidence: 98%

Reptile enamel matrix proteins: Selection, divergence, and functional constraint

Alazem

Abramyan

2019

J Exp Zool Pt B

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The three major enamel matrix proteins (EMPs): amelogenin (AMEL), ameloblastin (AMBN), and enamelin (ENAM), are intrinsically linked to tooth development in tetrapods. However, reptiles and mammals exhibit significant differences in dental patterning and development, potentially affecting how EMPs evolve in each group. In most reptiles, teeth are replaced continuously throughout life, while mammals have reduced replacement to only one or two generations. Reptiles also form structurally simple, aprismatic enamel while mammalian enamel is composed of highly organized hydroxyapatite prisms. These differences, combined with reported low sequence homology in reptiles, led us to predict that reptiles may experience lower selection pressure on their EMPs as compared with mammals. However, we found that like mammals, reptile EMPs are under moderate purifying selection, with some differences evident between AMEL, AMBN, and ENAM. We also demonstrate that sequence homology in reptile EMPs is closely associated with divergence times, with more recently diverged lineages exhibiting high homology, along with strong phylogenetic signal. Lastly, despite sequence divergence, none of the reptile species in our study exhibited mutations consistent with diseases that cause degeneration of enamel (e.g. amelogenesis imperfecta). Despite short tooth retention time and simplicity in enamel structure, reptile EMPs still exhibit purifying selection required to form durable enamel.

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Section: Methodsmentioning

confidence: 98%

Reptile enamel matrix proteins: Selection, divergence, and functional constraint

Alazem

Abramyan

2019

J Exp Zool Pt B

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“…The motif, domain, and catalytic sites of proteins/DNA could be identified by specifying these retained regions. 50 Therefore, this study aimed to analyze the miRNA target's correlation analysis with the other N‐region of SARS‐CoV‐2 Malaysia's strains and other N‐region of coronavirus strains. For this analysis, four types of SARS‐CoV‐2 Malaysia's strains with accession numbers MT372483.1, MT 372480.1, MT372481.1, and MT372482.1 were considered.…”

Section: Results Dan Discussionmentioning

confidence: 99%

“…Throughout evolution, specific sequences stay conserved. The motif, domain, and catalytic sites of proteins/DNA could be identified by specifying these retained regions 50 . Therefore, this study aimed to analyze the miRNA target's correlation analysis with the other N‐region of SARS‐CoV‐2 Malaysia's strains and other N‐region of coronavirus strains.…”

Section: Results Dan Discussionmentioning

confidence: 99%

MicroRNA of N‐region from SARS‐CoV‐2: Potential sensing components for biosensor development

Halim

Parmin

Hashim

et al. 2021

Biotech and App Biochem

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An oligonucleotide DNA probe has been developed for the application in the DNA electrochemical biosensor for the early diagnosis of coronavirus disease (COVID‐19). Here, the virus microRNA from the N‐gene of severe acute respiratory syndrome‐2 (SARS‐CoV‐2) was used for the first time as a specific target for detecting the virus and became a framework for developing the complementary DNA probe. The sequence analysis of the virus microRNA was carried out using bioinformatics tools including basic local alignment search tools, multiple sequence alignment from CLUSTLW, microRNA database (miRbase), microRNA target database, and gene analysis. Cross‐validation of distinct strains of coronavirus and human microRNA sequences was completed to validate the percentage of identical and consent regions. The percent identity parameter from the bioinformatics tools revealed the virus microRNAs’ sequence has a 100% match with the genome of SARS‐CoV‐2 compared with other coronavirus strains, hence improving the selectivity of the complementary DNA probe. The 30 mer with 53.0% GC content of complementary DNA probe 5′ GCC TGA GTT GAG TCA GCA CTG CTC ATG GAT 3′ was designed and could be used as a bioreceptor for the biosensor development in the clinical and environmental diagnosis of COVID‐19.

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A comparative analysis of multiple sequence alignments for biological data

Cited by 2 publications

References 18 publications

Reptile enamel matrix proteins: Selection, divergence, and functional constraint

Reptile enamel matrix proteins: Selection, divergence, and functional constraint

MicroRNA of N‐region from SARS‐CoV‐2: Potential sensing components for biosensor development

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