scholarly journals Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

10.5772/64325 ◽  
2016 ◽  
Author(s):  
Venkateswara R. Sripathi ◽  
Ramesh Buyyarapu ◽  
Siva P. Kumpatla ◽  
Abreeotta J. Williams ◽  
Seloame T. Nyaku ◽  
...  
Keyword(s):  
Structure And Function ◽  
Genomic Resources ◽  
Bioinformatics Tools ◽  
And Function

scholarly journals Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

2018 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada Ahmed Osman ◽  
Mohamed A. Hassan
Keyword(s):  
Familial Mediterranean Fever ◽  
In Silico ◽  
Mediterranean Basin ◽  
Mefv Gene ◽  
Structure And Function ◽  
Diagnostic Markers ◽  
Novel Mutations ◽  
Bioinformatics Tools ◽  
Mediterranean Fever ◽  
And Function

AbstractBackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.MethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.Result23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.ConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

scholarly journals Thirty five novel nsSNPs may effect on ADAMTS13 protein leading to Thrombotic thrombocytopenic purpura (TTP) using bioinformatics approach

2019 ◽  
Author(s):  
Tebyan A. Abdelhameed ◽  
Arwa I. Ahmed ◽  
Mujahed I. Mustafa ◽  
Amel N. Eltayeb ◽  
Fatima A. Abdelrhman ◽  
...  
Keyword(s):  
Thrombotic Thrombocytopenic Purpura ◽  
Nucleotide Substitution ◽  
Structure And Function ◽  
Biomedical Data ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Thrombocytopenic Purpura ◽  
Bioinformatics Tools ◽  
Life Threatening ◽  
And Function

ABSTRACTBackgroundGenetic polymorphisms in the ADAMTS13 gene are associated with thrombotic thrombocytopenic purpura or TTP, a life-threatening microangiopathic disorder. This study aims to predict the possible pathogenic SNPs of this gene and their impact on the protein structure and function using insilico methods.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms applied collectively to predictthe effect of single nucleotide substitution on both structure and function of the ADAMTS13 protein.ResultsFifty one mutations were found to be highly damaging to the structure and function of the protein. Of those, thirty five were novel nsSNPs not previously reported in the literature.ConclusionAccording to our analysis we found thirty five nsSNPs effects on ADAMTS13 protein leading to thrombotic thrombocytopenic purpura using computational approach. Bioinformatics tools are vital in prediction analysis, making use of increasingly voluminous biomedical data thereby providing markers for screening or for genetic mapping studies.

scholarly journals Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach

2019 ◽  
Author(s):  
Tebyan A. Abdelhameed ◽  
Mohamed Mustafa Osman Fadul ◽  
Dina Nasereldin Abdelrahman Mohamed ◽  
Amal Mohamed Mudawi ◽  
Sayaf Kamal Khalifa Fadul Allah ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Neurodegenerative Disorder ◽  
Structure And Function ◽  
Single Nucleotide Substitution ◽  
Single Nucleotide ◽  
Bioinformatics Tools ◽  
Tay Sachs Disease ◽  
Hexosaminidase A ◽  
And Function

ABSTRACTBackgroundGenetic polymorphisms in the HEXA gene are associated with a neurodegenerative disorder called Tay-Sachs disease (TSD) (GM2 gangliosidosis type 1). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of the hexosaminidase A protein.ResultsFifty nine mutations were found to be highly damaging to the structure and function of the HEXA gene protein.ConclusionAccording to this study, thirty two novel nsSNP in HEXA are predicted to have possible role in Tay-Saches Disease using different bioinformatics tools. Our findings could help in genetic study and diagnosis of Tay-Saches Disease.

scholarly journals Novel Deleterious nsSNPs within MEFV Gene that Could Be Used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using Bioinformatics Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A. Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada A. Osman ◽  
Mohamed A. Hassan
Keyword(s):  
Familial Mediterranean Fever ◽  
In Silico ◽  
Mediterranean Basin ◽  
Mefv Gene ◽  
Structure And Function ◽  
Diagnostic Markers ◽  
Novel Mutations ◽  
Bioinformatics Tools ◽  
Mediterranean Fever ◽  
And Function

Background. Familial Mediterranean Fever (FMF) is the most common autoinflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin. We aimed to identify the pathogenic SNPs in MEFV by computational analysis software. Methods. We carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function. Result. 23 novel mutations out of 857 nsSNPs are found to have deleterious effect on the MEFV structure and function. Conclusion. This is the first in silico analysis of MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

scholarly journals The Association between SLC25A15 Gene Polymorphisms and Hyperornithinemia-hyperammonemia-homocitrullinuria Syndrome: Using In Silico Analysis

2019 ◽  
Author(s):  
Nuha A. Mahmoud ◽  
Dina T. Ahmed ◽  
Zainab O. Mohammed ◽  
Fatima A. Altyeb ◽  
Mujahed I. Mustafa ◽  
...  
Keyword(s):  
In Silico ◽  
Autosomal Recessive ◽  
Urea Cycle ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Medical Testing ◽  
Bioinformatics Tools ◽  
And Function ◽  
Silico Analysis ◽  
Selection Of

BackgroundHyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome is an autosomal recessive inborn error of the urea cycle. It is caused by mutations in the SLC25A15 gene that codes the mitochondrial ornithine transporter. The aim of this study is to detect and identify the pathogenic SNPs in SLC25A15 gene through a combination set of bioinformatics tools and their effect on the structure and function of the protein.MethodsThe deleterious SNPs in SLC25A15 are detected by various bioinformatics tools, with addition to identifying their effects on the structure and function of this gene.Results20 deleterious SNPs out 287of were found to have their own damaging effects on the structure and function of the SLC25A15 gene.ConclusionThis study is the first in silico analysis of SLC25A15 using a selection of bioinformatics tools to detect functional and structural effects of deleterious SNPs. Finding the pathogenic SNPs is a promising start to innovate new, useful SNP diagnostic markers for medical testing and for safer novel therapies specifically targeting mutant SLC25A15.

scholarly journals In silicoanalysis of coding SNPs and 3′-UTR associated miRNAs inDCAF17gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome

2019 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Asia M. Elrashied ◽  
Alaa I. Mohammed ◽  
Sara A. Mirghani ◽  
Rania E. Osman ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Protein Structure ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Novel Mutations ◽  
Inherited Disorders ◽  
Bioinformatics Tools ◽  
Extrapyramidal Signs ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundWoodhouse-Sakati Syndrome refers to a group of inherited disorders characterized by alopecia, hypogonadism, diabetes mellitus, hypothyroidism and progressive extrapyramidal signs. The aim of this study is to identify the pathogenic SNPs in theDCAF17gene with their related mciroRNAs and their effect on the structure and function of the protein.Material and MethodsWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. After that we defined the miRNAs founded in the 3′-UTR region on theDCAF17gene and studied the annotations relative to it.ResultsTen deleterious SNPs out of 339 were found to have a damaging effect on the protein structure and function, with one significant micoRNA in the 3′-UTR region.ConclusionThis was the first in silico analysis ofDCAF17gene, in which 10 novel mutations were found using different bioinformatics tools that could be used as a diagnostic markers for Woodhouse-Sakati syndrome, with one relevant microRNA that can regulate the function of the protein.

scholarly journals In silico analysis ofIDH3Agene revealed Novel mutations associated with Retinitis Pigmentosa

2019 ◽  
Author(s):  
Thwayba A. Mahmoud ◽  
Abdelrahman H. Abdelmoneim ◽  
Naseem S. Murshed ◽  
Zainab O. Mohammed ◽  
Dina T. Ahmed ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
In Silico ◽  
In Silico Analysis ◽  
Photoreceptor Cells ◽  
Structure And Function ◽  
Novel Mutations ◽  
Inherited Disorders ◽  
Bioinformatics Tools ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundRetinitis Pigmentosa (RP) refers to a group of inherited disorders characterized by the death of photoreceptor cells leading to blindness. The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein.Methodwe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function.Conclusionthis is the first in silico analysis of IDH3A gene and 20 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for Retinitis Pigmentosa.

scholarly journals Comprehensive Analysis of HEXB Protein Reveal Forty Two Novel nsSNPs That May Lead to Sandhoff disease (SD) Using Bioinformatics

2019 ◽  
Author(s):  
Tebyan A. Abdelhameed ◽  
Mosab M. Gasmelseed ◽  
Mujahed I. Mustafa ◽  
Dina N. Abdelrahman ◽  
Fatima A. Abdelrhman ◽  
...  
Keyword(s):  
Neurodegenerative Disorder ◽  
Sandhoff Disease ◽  
Structure And Function ◽  
Beta Subunit ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Bioinformatics Tools ◽  
Hexosaminidase A ◽  
And Function ◽  
Hexb Gene

ABSTRACTBackgroundSingle Nucleotide Polymorphisms (SNPs) in the HEXB gene are associated with a neurodegenerative disorder called Sandhoff disease (SD) (GM2 gangliosidosis-O variant). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of beta subunit beta subunit of both hexosaminidase A and hexosaminidase B proteins.ResultsForty nine mutations were found to be extremely damaging to the structure and function of the HEXB gene protein.ConclusionAccording to this study, forty two novel nsSNP in HEXB are predicted to have possible role in Sandhoff disease using different bioinformatics tools, beside two SNPs found to have effect on miRNAs binding site affecting expression of HEXB gene. Our findings may assist in genetic study and diagnosis of Sandhoff disease.

scholarly journals In Silico Analysis and Modeling of Novel Pathogenic Single Nucleotide Polymorphisms (SNPs) in Human CD40LG Gene

2019 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Mujahed I. Mustafa ◽  
Thwayba A. Mahmoud ◽  
Naseem S. Murshed ◽  
Mohamed A. Hassan
Keyword(s):  
In Silico ◽  
Elevated Serum ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Immunoglobulin M ◽  
Hyper Igm Syndrome ◽  
Bioinformatics Tools ◽  
Hyper Igm ◽  
And Function ◽  
Silico Analysis

Abstract:Background:The X-linked hyper-immunoglobulin M syndrome (XHIGM) is a rare, inherited immune deficiency disorder. It is more common in males. Characterized by elevated serum IgM levels and low to undetectable levels of serum IgG, IgA and IgE. Hyper-IgM syndrome is caused by mutations in the CD40LG gene. Located in human Xq26. CD40LG acts as an immune modulator in activated T cells.Method:We used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result:8 novel SNPs out of 233 were found to have most deleterious effect on the protein structure and function. While modeling of nsSNPs was studied by Project HOPE software.Conclusion:Better understanding of Hyper-IgM syndrome caused by mutations in CD40LG gene was achieved using in silico analysis. This is the first in silico functional analysis of CD40LG gene and 8 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for hyper-IgM syndrome. These 8 novel SNPs may be important candidates for the cause of different types of human diseases by CD40LG gene.

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