scholarly journals Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis

2008 ◽  
Vol 10 (1) ◽  
pp. 11-23 ◽  
Author(s):  
M. R. Aniba ◽  
S. Siguenza ◽  
A. Friedrich ◽  
F. Plewniak ◽  
O. Poch ◽  
...  
Keyword(s):  
Expert Systems ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Proof Of Concept ◽  
Multiple Sequence ◽  
Knowledge Based

scholarly journals KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

2015 ◽  
Vol 32 (6) ◽  
pp. 932-936 ◽  
Author(s):  
Joanna Lange ◽  
Lucjan S. Wyrwicz ◽  
Gert Vriend
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Active Sites ◽  
Intrinsically Disordered Proteins ◽  
Tertiary Structure ◽  
Substitution Matrix ◽  
Disordered Proteins ◽  
Multiple Sequence ◽  
Intrinsically Disordered ◽  
Knowledge Based

Abstract Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: [email protected]

scholarly journals AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

2010 ◽  
Vol 38 (19) ◽  
pp. 6338-6349 ◽  
Author(s):  
M. R. Aniba ◽  
O. Poch ◽  
A. Marchler-Bauer ◽  
J. D. Thompson
Keyword(s):  
Expert System ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence ◽  
Knowledge Based

scholarly journals Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

2010 ◽  
Vol 38 (21) ◽  
pp. 7353-7363 ◽  
Author(s):  
M. R. Aniba ◽  
O. Poch ◽  
J. D. Thompson
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence

scholarly journals A time warping approach to multiple sequence alignment

2017 ◽  
Vol 16 (2) ◽  
Author(s):  
Ana Arribas-Gil ◽  
Catherine Matias
Keyword(s):  
Sequence Alignment ◽  
Functional Data Analysis ◽  
Multiple Sequence Alignment ◽  
Functional Data ◽  
Dynamic Time Warping ◽  
Proof Of Concept ◽  
Time Warping ◽  
Synthetic Experiment ◽  
Multiple Sequence ◽  
Dynamic Time

AbstractWe propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a median path that represents the MSA we are looking for. We establish a proof of concept that our method could be an interesting ingredient to include into refined MSA techniques. We present a simple synthetic experiment as well as the study of a benchmark dataset, together with comparisons with 2 widely used MSA softwares.

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

2020 ◽  
Vol 17 (1) ◽  
pp. 59-77
Author(s):  
Anand Kumar Nelapati ◽  
JagadeeshBabu PonnanEttiyappan
Keyword(s):  
Uric Acid ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Multiple Sequence ◽  
Physiochemical Properties ◽  
Pharmaceutical Industries

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.

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

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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