Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment

Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

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LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

Current Nutrition & Food Science ◽

10.2174/1573401314666180223143523 ◽

2019 ◽

Vol 15 (4) ◽

pp. 353-362

Author(s):

Sambhaji B. Thakar ◽

Maruti J. Dhanavade ◽

Kailas D. Sonawane

Keyword(s):

Phylogenetic Analysis ◽

Medicinal Plants ◽

Homology Modeling ◽

Sequence Alignment ◽

Vigna Unguiculata ◽

Multiple Sequence Alignment ◽

Legume Species ◽

Mangrove Species ◽

Multiple Sequence ◽

Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

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A Hierarchical Classification for the Selection of the Most Suitable Multiple Sequence Alignment Methodology

Current Bioinformatics ◽

10.2174/157489361002150518145112 ◽

2015 ◽

Vol 10 (2) ◽

pp. 199-207

Author(s):

Francisco Ortuño ◽

Hector Pomares ◽

Olga Valenzuela ◽

Carolina Torres ◽

Ignacio Rojas

Keyword(s):

Sequence Alignment ◽

Multiple Sequence Alignment ◽

Hierarchical Classification ◽

Multiple Sequence ◽

Selection Of

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Fast DNA Sequence Alignment Algorithm Based on Quality Score Using Improved Dynamic Programming and Fuzzy Gap Cost Control

Current Bioinformatics ◽

10.2174/1574893609666140523000227 ◽

2014 ◽

Vol 9 (5) ◽

pp. 540-547

Author(s):

Kwang Kim ◽

Hyun Park ◽

Doo Song

Keyword(s):

Dynamic Programming ◽

Dna Sequence ◽

Sequence Alignment ◽

Cost Control ◽

Quality Score ◽

Alignment Algorithm ◽

Sequence Alignment Algorithm ◽

Dna Sequence Alignment ◽

Improved Dynamic Programming

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