COMPUTATIONAL ANALYSIS FOR SEQUENCE ALIGNMENT AND PHYLOGENETIC ANALYSIS OF HUMAN HERPES VIRUS (original) (raw)
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Sequence alignment is a prerequisite for biological sequence data analysis. In this paper, a systematic approach used to analyze the four proteins from Viral Capsid of Human Herpes Virus (HSV) which cause cytomegalovirus, brain infl ammation, and lifelong infection. It is not viable to extend the relationship between drug-viral protein interactions of individual protein of HSV. With objective to develop the broad spectrum antibiotics, it is necessary to analyze the protein alignment and similarity. So the various point accepted scoring matrices (PAM) used for Capsid protein sequence alignment using Bioinformatics Tool of Matrix laboratory (Mat lab). This paper highlights the optimization of scoring matrices of aligned sequences and best scores for the different strain of HSV. From results showed that lower PAM matrix is suitable for capsid proteins of HSV-1 and HSV-2 due to closely related proteins of HSV. The results of sequence alignment can assist in the drug development and help to reduce the infection using antiviral therapy.
Sequence Alignment of Triplex Capsid Protein of Human Herpes Simplex Virus
Sequence comparison positioned at the centre of bioinformatics analysis. It is an important step toward structural and functional analysis of sequences. Pair wise sequence and multiple sequence alignment are the techniques of aligning the sequences on basis of database similarity. In first section this paper, we performed the pair wise alignment of viral capsid proteins of human herpes simplex virus (HHV) using heuristic and dynamic algorithm. In second part we implemented exact method, progressive alignment and iterative approach for multiple sequence alignment of viral protein data. The results from our experiments demonstrate that the multiple sequence alignment is more sensitive method than pair wise alignment can be used as an efficient computational platform for high performance sequence alignment applications. In later section of the paper we performed multiple sequence alignment of viral protein with hidden markov model (HMM).
International Journal
Protein sequence alignment has become an informative tool in modern molecular biology research. A number of substitution matrices have been readily available for sequence alignments, but it is challenging task to compute optimal matrices for alignment accuracy. Here, we used the parameter optimization procedure to select the optimal Q of substitution matrices for major viral capsid protein of human herpes simplex virus. Results predict that Blosum matrix is most accurate on alignment benchmarks, and Blosum 60 provides the optimal Q in all substitution matrices. PAM 200 matrices results slightly below than Blosum 60, while VTML matrices are intermediate of PAM and VT matrices under dynamic programming.
American Journal of Biomedical Science & Research, 2019
Abstract Bioinformatics is an interdisciplinary field mainly involving molecular genetics. computer science, mathematics, and statistics. Data intensive and large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. In this study we used bioinformatics as a tool to study homology between Herpes simplex virus type 1 glycoprotein C gene and Herpes simplex virus type 2glycoprotein F gene. In the beginning we used the Gene data Bank to get the DNA sequence. Then we used a program Blast and got a percentage alignment 81%. We used protein data bank (PDB) to estimate the structure of the expressed proteins that were tertiary (three dimensional) structure that harbor both α helices and β pleated sheets. Finally, we used “PHYRE2 “protein folding recognition set to visualize, analyze and manipulate the resulted 3D protein model.
Identification of structural protein–protein interactions of herpes simplex virus type 1
Virology, 2008
In this study we have defined protein-protein interactions between the structural proteins of herpes simplex virus type 1 (HSV-1) using a LexA yeast two-hybrid system. The majority of the capsid, tegument and envelope proteins of HSV-1 were screened in a matrix approach. A total of 40 binary interactions were detected including 9 out of 10 previously identified tegument-tegument interactions (Vittone, V., Diefenbach, E., Triffett, D., Douglas, M.W., Cunningham, A.L., and Diefenbach, R.J., 2005. Determination of interactions between tegument proteins of herpes simplex virus type 1. J. Virol. 79, 9566-9571). A total of 12 interactions involving the capsid protein pUL35 (VP26) and 11 interactions involving the tegument protein pUL46 (VP11/12) were identified. The most significant novel interactions detected in this study, which are likely to play a role in viral assembly, include pUL35-pUL37 (capsid-tegument), pUL46-pUL37 (tegumenttegument) and pUL49 (VP22)-pUS9 (tegument-envelope). This information will provide further insights into the pathways of HSV-1 assembly and the identified interactions are potential targets for new antiviral drugs.
Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics
2003
The dispositions of 39 α helices of greater than 2.5 turns and four β sheets in the major capsid protein (VP5, 149 kDa) of herpes simplex virus type 1 were identified by computational and visualization analysis from the 8.5 Å electron cryomicroscopy structure of the whole capsid. The assignment of helices in the VP5 upper domain was validated by comparison with the recently determined crystal structure of this region.
2011
Protein and nucleotide distance methods are among the most commonly used methods for evolutionary analysis from sequence data. Pairwise DNA and protein sequence alignment is an input data for computational biology. This work is the focus on best substitution model among protein and genetic model of human herpes simplex virus, which cause numerous infection to a human being through DNA maturation. In the present study, we have selected major, minor and triplex capsid region nucleotide sequences and major capsid protein of human herpes simplex virus for the substitution model analysis. The main objective of the work is to assess the genetic and proteomic variations among the minor, major and triplex capsid regions of human herpes simplex virus.
Molecular phylogenetic is a fundamental aspect of evolutionary analysis and depends on distance & character based methods. In this paper, we compare the viral capsid proteins of HHV to analyze the relationship among proteins using substitution models, phylogenetic model with exhaustive search and ME techniques. The effect of Poisson correction with shape parameter on NJ and UPGMA trees also analyze. We show by extensive computer simulation that phylogenetic tree is the reflection of substitution distance. The effect of max-mini branch & bound method and minimini heuristic model and log likelihood associated with character based tree also discussed. We applied ML and MP for perfectly analysis of proteins relationship. We conclude that substitution models, shape parameter, search level and SBL have a critical role to reconstruct phylogenetic tree. Molecular clock study shows that χ 2 value is higher in closely as compare distant related proteins.