In silico bioinformatic tools for determining core genes from sets of genomes

2010 ◽  
Vol 72 (2) ◽  
pp. 147-152
Author(s):  
Padmanabhan Mahadevan ◽  
Donald Seto
Keyword(s):  
In Silico ◽  
Bioinformatic Tools ◽  
Core Genes

Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using In silico Method

2012 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Mohd Fakharul Zaman Raja Yahya ◽  
Hasidah Mohd Sidek
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Nuclear Export ◽  
Nuclear Export Signal ◽  
Plasmodium Species ◽  
Mitogen Activated Protein Kinase ◽  
Multiple Sequence ◽  
Bioinformatic Tools ◽  
Wide Range ◽  
Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range ofhosts including humans and rodents. There are two copies ofmitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise ofpresented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series ofpublicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localizedandcontain both a nuclear localization signal (NLS) anda Leucine-rich nuclear export signal (NES). The activation motifs ofTDYand TSH werefound to befully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection ofa multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising ofdifferent amino acids present in MAPK1 and MAPK2 respectively, with respect to rodent and human Plasmodia. 1t is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

scholarly journals Cloning, Sequencing, and In Silico Analysis of β-Propeller Phytase Bacillus licheniformis Strain PB-13

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Vinod Kumar ◽  
Gopal Singh ◽  
Punesh Sangwan ◽  
A. K. Verma ◽  
Sanjeev Agrawal
Keyword(s):  
Phylogenetic Tree ◽  
Bacillus Licheniformis ◽  
In Silico ◽  
Catalytic Mechanism ◽  
Specific Activity ◽  
In Silico Analysis ◽  
Homology Search ◽  
Multiple Sequence ◽  
Bioinformatic Tools ◽  
C Terminus

β-Propeller phytases (BPPhy) are widely distributed in nature and play a major role in phytate-phosphorus cycling. In the present study, a BPPhy gene from Bacillus licheniformis strain was expressed in E. coli with a phytase activity of 1.15 U/mL and specific activity of 0.92 U/mg proteins. The expressed enzyme represented a full length ORF “PhyPB13” of 381 amino acid residues and differs by 3 residues from the closest similar existing BPPhy sequences. The PhyPB13 sequence was characterized in silico using various bioinformatic tools to better understand structural, functional, and evolutionary aspects of BPPhy class by multiple sequence alignment and homology search, phylogenetic tree construction, variation in biochemical features, and distribution of motifs and superfamilies. In all sequences, conserved sites were observed toward their N-terminus and C-terminus. Cysteine was not present in the sequence. Overall, three major clusters were observed in phylogenetic tree with variation in biophysical characteristics. A total of 10 motifs were reported with motif “1” observed in all 44 protein sequences and might be used for diversity and expression analysis of BPPhy enzymes. This study revealed important sequence features of BPPhy and pave a way for determining catalytic mechanism and selection of phytase with desirable characteristics.

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

2007 ◽  
Vol 68 (1) ◽  
pp. 19-32 ◽  
Author(s):  
Helge Küster ◽  
Anke Becker ◽  
Christian Firnhaber ◽  
Natalija Hohnjec ◽  
Katja Manthey ◽  
...  
Keyword(s):  
In Silico ◽  
Transcriptome Profiling ◽  
Bioinformatic Tools ◽  
Est Sequencing

scholarly journals Applying Bioinformatic Platforms, In Vitro, and In Vivo Functional Assays in the Characterization of Genetic Variants in the GH/IGF Pathway Affecting Growth and Development

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2063
Author(s):  
Sabina Domené ◽  
Paula A. Scaglia ◽  
Mariana L. Gutiérrez ◽  
Horacio M. Domené
Keyword(s):  
In Silico ◽  
Growth And Development ◽  
Genetic Variant ◽  
Modeling Tools ◽  
In Vivo Models ◽  
Bioinformatic Tools ◽  
Functional Assays

Heritability accounts for over 80% of adult human height, indicating that genetic variability is the main determinant of stature. The rapid technological development of Next-Generation Sequencing (NGS), particularly Whole Exome Sequencing (WES), has resulted in the characterization of several genetic conditions affecting growth and development. The greatest challenge of NGS remains the high number of candidate variants identified. In silico bioinformatic tools represent the first approach for classifying these variants. However, solving the complicated problem of variant interpretation requires the use of experimental approaches such as in vitro and, when needed, in vivo functional assays. In this review, we will discuss a rational approach to apply to the gene variants identified in children with growth and developmental defects including: (i) bioinformatic tools; (ii) in silico modeling tools; (iii) in vitro functional assays; and (iv) the development of in vivo models. While bioinformatic tools are useful for a preliminary selection of potentially pathogenic variants, in vitro—and sometimes also in vivo—functional assays are further required to unequivocally determine the pathogenicity of a novel genetic variant. This long, time-consuming, and expensive process is the only scientifically proven method to determine causality between a genetic variant and a human genetic disease.

scholarly journals Genetics A Comprehensive In Silico Analysis of Deleterious SNPs of Paraplegin Protein Associated with Hereditary Spastic Paraplegia through Mitochondrial Dysfunction

2020 ◽  
Vol 2 (2) ◽  
pp. 1-14
Author(s):  
Ammara Akhtar ◽  
Sobia Nazir Choudhry ◽  
Rana Muhammad Mateen ◽  
Mureed Hussain
Keyword(s):  
Hereditary Spastic Paraplegia ◽  
In Silico ◽  
Mitochondrial Protein ◽  
In Silico Analysis ◽  
Missense Mutations ◽  
Spastic Paraplegia ◽  
Bioinformatic Tools ◽  
Pathogenic Variants ◽  
Structural And Functional Properties ◽  
Silico Analysis

Hereditary spastic paraplegia (HSP) is a heterogenous neurological disorder primarily associated with progressive spasticity. Paraplegin is a mitochondrial protein and mutations in this protein can lead to HSP. In this study, in silico analysis was carried out to identify the pathogenic variants of SPG7 (paraplegin protein). To find novel pathogenic mutations, missense and splicing variants were collected from gnomAD database and passed through a detailed and stringent analysis with the help of a variety of bioinformatic tools. The list of mutations was examined and compared in ClinVar. Altogether, 14 missense mutations and 18 splicing mutations were obtained and these mutations were predicted to have the potential of disrupting the normal structural and functional properties of paraplegin protein.

scholarly journals In Silico Molecular Studies of Antiophidic Properties of the Amazonian Tree Cordia nodosa Lam.

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4160
Author(s):  
Luzuriaga-Quichimbo ◽  
Blanco-Salas ◽  
Muñoz-Centeno ◽  
Peláez ◽  
Cerón-Martínez ◽  
...  
Keyword(s):  
Latin American ◽  
In Silico ◽  
Biological Diversity ◽  
Binding Free Energy ◽  
Molecular Structures ◽  
Convention On Biological Diversity ◽  
Bioinformatic Tools ◽  
Bothrops Asper ◽  
Bothrops Atrox ◽  
Bothrops Pirajai

We carried out surveys on the use of Cordia nodosa Lam. in the jungles of Bobonaza (Ecuador). We documented this knowledge to prevent its loss under the Framework of the Convention on Biological Diversity and the Nagoya Protocol. We conducted bibliographic research and identified quercetrin as a significant bioactive molecule. We studied its in silico biological activity. The selected methodology was virtual docking experiments with the proteins responsible for the venomous action of snakes. The molecular structures of quercetrin and 21 selected toxins underwent corresponding tests with SwissDock and Chimera software. The results point to support its antiophidic use. They show reasonable geometries and a binding free energy of −7 to −10.03 kcal/mol. The most favorable values were obtained for the venom of the Asian snake Naja atra (5Z2G, −10.03 kcal/mol). Good results were also obtained from the venom of the Latin American Bothrops pirajai (3CYL, –9.71 kcal/mol) and that of Ecuadorian Bothrops asper snakes (5TFV, –9.47 kcal/mol) and Bothrops atrox (5TS5, –9.49 kcal/mol). In the 5Z2G and 5TS5 L-amino acid oxidases, quercetrin binds in a pocket adjacent to the FAD cofactor, while in the myotoxic homologues of PLA2, 3CYL and 5TFV, it joins in the hydrophobic channel formed when oligomerizing, in the first one similar to α-tocopherol. This study presents a case demonstration of the potential of bioinformatic tools in the validation process of ethnobotanical phytopharmaceuticals and how in silico methods are becoming increasingly useful for sustainable drug discovery.

scholarly journals M&Ms: A software for building realistic Microbial Mock communities

2021 ◽  
Author(s):  
Natalia García-García ◽  
Javier Tamames ◽  
Fernando Puente-Sánchez
Keyword(s):  
Microbial Communities ◽  
In Silico ◽  
Source Code ◽  
Simulated Data ◽  
Bioinformatic Tools ◽  
Sequencing Technologies ◽  
Bioinformatic Tool ◽  
Reference Sequences ◽  
User Friendly ◽  
Mock Communities

Motivation: Advances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze these data. As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions. Although there is a large amount of software dedicated to produce reads from in silico microbial communities, often the simulated data diverge widely from real situations. Results: Here, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce realistic amplicon datasets from reference sequences, based on pragmatic ecological parameters. This tool creates sequence libraries for in silico microbial communities with user-controlled richness, evenness, microdiversity, and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. M&Ms also provides additional figures and files with extensive details on how each synthetic community is composed, so that users can make informed choices when designing their benchmarking pipelines. Availability: The source code of M&Ms is freely available from https://github.com/ggnatalia/MMs

scholarly journals In silico analysis of deleterious SNPs of human MTUS1 gene and their impacts on subsequent protein structure and function

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252932
Author(s):  
Liza Teresa Rozario ◽  
Tanima Sharker ◽  
Tasnin Akter Nila
Keyword(s):  
Tumor Suppressor ◽  
In Silico ◽  
Individualized Medicine ◽  
Large Population ◽  
In Silico Analysis ◽  
Population Based ◽  
Bioinformatic Tools ◽  
Functional Snps ◽  
Wide Range ◽  
And Function

The mitochondrial tumor suppressor 1 (MTUS1) gene acts as a crucial tumor suppressor by inhibiting growth and proliferation of eukaryotic cells including tumor cell lines. Down regulation of MTUS1 gene has been implicated in a wide range of cancers as well as various human diseases. Alteration through nsSNPs can potentially damage the structure and/or function of the protein. As characterization of functional SNPs in such disease linked genes is a major challenge, it is feasible to analyze putative functional SNPs prior to performing larger population studies. Hence, in this in silico study we differentiated the potentially harmful nsSNPs of the MTUS1 gene from the neutral ones by using various sequence and structure based bioinformatic tools. In a total of 215 nsSNPs, 9 were found to be most likely to exert deleterious effect using 7 prediction tools. From which, 5nsSNPs (S1259L, E960K, P503T, L1084V and L1143Q) were selected as potentially damaging due to their presence in the highly conserved region and ability to decrease protein stability. In fact, 2 nsSNPs (S1259L and E960K) among these 5 were found to be individually associated with two distinctive cancers named Stomach adenocarcinoma and Uterine corpus endometrial carcinoma. As this is the first comprehensive study analyzing the functional nsSNPs of MTUS1, the results of the current study would certainly be helpful in future prospects concerning large population-based studies as well as drug discovery, especially developing individualized medicine.

Sign in / Sign up

Export Citation Format

Share Document