Multiple Sequence Alignment of Bioinformatics

Bioinformatics is an interdisciplinary area of research, which also plays a vital role in the field of agriculture based studies. Tools of bioinformatics provides significant role in agriculture research. Present paper is also focusing on agriculture informatics. As we know using bioinformatics tool we can explore many more hidden information from agriculture data. In this paper we had applied CLUSTAL O tool for multiple sequence alignment of nine different model plants have same protein glycogen synthase. We had constructed phylogenetic tree for investigating relationship between model plants neighbor -joining tree without distance corrections by CLUSTAL O tool.


I. INTRODUCTION
Bioinformatics is a fresh field of science but it is making evolution in each field of biotechnology has its diligence in the drug by providing the genome information of different organisms, likewise agriculture has also taken benefit of this fiel microorganisms play significant function and bioinformatics provides complete information of these organisms [1sequencing of the plants and animals has benefits to agriculture [10]. We care about the sequence alignments in the computational biology because it gives biologists functional information about [11]. For example, it can tell us about the evolution of the organisms, we can see which realms derived protein) are vulnerable to mutation and which can have one rest replaced by another without function, we can analyse homologous genes and can paralogs and orthologs genes that are evolutionary connected. In problems such as the evolutionary tree relates on sequence data, or in protein engineering, where a multiple alignment of related sequences may often give way the good number information on the design of a new protein, a molecular biologist must evaluate more than two sequences concurrently [12][13][14][15][16][17][18][19]. A multiple sequence alignment (MSA) arranges protein sequences into a rectangular array with the objective that residues in a given column are homologous (derived from a single position in an ancestral sequence), identical (in a rigid local structural alignment) or participate a common functional role these three criterions are fundamentally closely related proteins, sequence, structure and function Bioinformatics is an interdisciplinary area of research, which also plays a vital role in the field of Tools of bioinformatics provides significant role in agriculture research. Present paper is also matics. As we know using bioinformatics tool we can explore many more hidden information from agriculture data. In this paper we had applied CLUSTAL O tool for multiple sequence alignment of nine different model plants have same protein glycogen We had constructed phylogenetic tree for ween model plants using joining tree without distance corrections method lignment, Phylogenetic NTRODUCTION field of science but it is making field of biotechnology incredibly. As it by providing the genome likewise the field of of this field because function in agriculture complete genomic -9]. The genome s has too provided We care about the sequence alignments in the computational biology because it gives information about diverse aspects . For example, it can tell us about the evolution of the realms of a gene (or its to mutation and which can replaced by another without altering enes and can reveal rthologs genes that are evolutionary . In problems such as the building of an on sequence data, or in protein engineering, where a multiple alignment of related way the good number helpful information on the design of a new protein, a molecular more than two sequences . A multiple sequence alignment (MSA) arranges protein sequences into a rectangular array that residues in a given column are homologous (derived from a single position in an ancestral (in a rigid local structural alignment) a common functional role [20]. Although corresponding for closely related proteins, sequence, structure and function deviate over evolutionary time and result in unlike alignments [21] alignments continue to be superior to methods; there is therefore a improve the biological correctness Moreover, the high computational cost of most naive algorithms motivates improvements in speed and memory usage to contain the rapid increase i data [22][23][24][25].
In this paper we will perform multiple sequence alignment for glycogen synthase protein of nine different plants [26].
Glycogen synthase is an converting glucose to glycogen. It takes glucose and converts them into long polymers of gly [27]. In other words, this enzyme converts surplus glucose residues one by one into a polymeric for storage as glycogen. Glycogen synthase concentration is highest in the bloodstream 30 to 60 minute intense exercise. It is a key enzyme in 31].
There are various tools available for multiple sequence alignment. Some frequently used tools are listed below in Table 1. . Manually sophisticated alignments continue to be superior to solely automated methods; there is therefore an unremitting effort to correctness of MSA tools. , the high computational cost of most naive algorithms motivates improvements in speed and memory the rapid increase in accessible sequence In this paper we will perform multiple sequence alignment for glycogen synthase protein of nine different is an enzyme concerned in . It takes petite polymers of glucose and converts them into long polymers of glycogen . In other words, this enzyme converts one by one into a polymeric chain . Glycogen synthase concentration is highest in the bloodstream 30 to 60 minute following intense exercise. It is a key enzyme in glycogenesis [28-  phylogenetic analysis and we can use it as input for other bioinformatics MSA) is a sequence biological sequences, loads of cases, the input set of query sequences are an evolutionary affiliation by which they lineage and are descended from a From the consequential MSA, sequence homology can be incidental and phylogenetic study can be conducted to review the sequences alignment is frequently used to assess sequence preservation of protein domains, tertiary and secondary structures, and amino acid or nucleotides [35].

A. Multiple Sequence Alignment
Multiple sequence alignment also refer to the procedure of aligning such a sequences of biologically applicable length can be tricky and are almost always prolonged to align by hand, computational algorithms are used fabricate and analyze the alignment. MSAs necessitate more sophisticated methodologies that because they are more computationally complex.
The majority of multiple sequence alignment programs use heuristic methods rather than optimization because distinguishing alignment between more than a few sequences of reasonable length is prohibitively computationally expensive [36].

Agriculture Innovations and Research Volume 4, Issue 5, ISSN (Online) 2319-1473
set of query sequences are unspecified to have by which they contribute to a lineage and are descended from a universal ancestor [34]. From the consequential MSA, sequence homology can be incidental and phylogenetic study can be conducted to review the sequences alignment is frequently used to assess sequence preservation of protein domains, tertiary es, and amino acid or nucleotides Multiple sequence alignment also refer to the procedure of aligning such a sequences of biologically applicable length can be tricky and are almost always prolonged to align by hand, computational algorithms are used to fabricate and analyze the alignment. MSAs necessitate more sophisticated methodologies that pair wise alignment because they are more computationally complex. multiple sequence alignment programs methods rather than global distinguishing the most favorable Sequence alignment produced by CLUSTAL O program, of above protein sequences is a key denoting conserved sequence (*), conservative mutations conservative mutation (.), and non-conservative mutations ().
In biology, conserved sequences are analogous or indistinguishable sequences that place within nucleic acid sequences, protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within dissimilar molecules formed by the similar organism (paralogous sequences).
In the case of cross species preservation that a meticulous sequence may have been maintained by evolution despite speciation.
The further support the phylogenetic tree a particular conserved sequences may occur the more highly conserved it is said to be. Because sequence information is normally carried from parents to progeny by genes, a conserved sequence involves that there is gene; whereas conservative mutations are mutations that alter an amino acid to a diverse amino acid with alike biochemical properties (eg. charge, hydrophobicity and In biology, conserved sequences are analogous or indistinguishable sequences that place within nucleic acid sequences, protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within dissimilar molecules formed by the s). preservation, this indicates sequence may have been maintained by The further support the phylogenetic tree a particular conserved sequences may occur the more highly conserved it is said to be. Because sequence information is normally carried from parents to progeny by genes, a conserved sequence involves that there is a conserved conservative mutations are mutations that alter an amino acid to a diverse amino acid with alike biochemical properties (eg. charge, hydrophobicity and size). Conservative mutations in proteins often have a lesser consequence on function than non mutations. The compact outcome mutations on function can also be seen in the dissimilar mutations in nature. Non mutations between proteins are far more detached by natural selection effects [37].

A. Phylogenetic Tree
A phylogenetic tree or evolutionary tree is a furcating illustration or tree viewing the condition association between diverse biological species or other entities.
Their phylogeny based on similarities and deviations in their physical or genetic uniqueness. The taxa connected mutually in the tree are indirect to have descended from a same root.
Phylogenetic trees are essential to the area of phylogenetics. This phylogenetic tree is constructed by Neighbour-joining tree without distance correction method by CLISTAL O program [39].

Agriculture Innovations and Research Volume 4, Issue 5, ISSN (Online) 2319-1473
Conservative mutations in proteins often have a unction than non-conservative outcome of conservative mutations on function can also be seen in the incidence of mutations in nature. Non-conservative mutations between proteins are far more probable to be natural selection due to their venomous A phylogenetic tree or evolutionary tree is a furcating illustration or tree viewing the condition evolutionary association between diverse biological species or other Their phylogeny based on similarities and deviations in their physical or genetic uniqueness. The taxa connected indirect to have descended from a Phylogenetic trees are essential to the area of phylogenetics. This phylogenetic tree is constructed by joining tree without distance correction method Copyright © 2016 IJAIR, All right reserved A cladogram derived from Greek clados "branch" and gramma "character", is a map used in cladistics analysis which shows associations between organisms. A cladogram is not; however, an evolutionary tree since it does not show how ancestors are related to offspring or how much they have distorted. Many evolutionary trees can be indirect from a particular cladogram. A cladogram uses lines that devise off in dissimilar directions ending a clade, groups of organisms with a concluding common ancestor. There are many builds of cladograms but they all have lines that branch off from supplementary lines. The lines can be followed back to where they branch off. These branching off points symbolize a hypothetical ancestor (not a genuine entity) which is inferred to display the traits shared between the concluding taxa above it. This hypothetical ancestor might then supply clues about the arrangement of evolution of diverse features, alterati and other evolutionary narratives about ancestors. Even if conventionally such cladograms were generated mostly on the basis of morphological typescript, DNA and RNA sequencing data and computational phylogenetics are nowadays extremely used in the generation of cladograms, either on their own or in amalgamation with morphology [40].

IV. CONCLUSION
We had concluded with above study that tool can be used for multiple sequence alignment for all nine model plants from different families generate phylogenetic tree from the same tool. one can view the relations among model plants having same protein and from result of multiple sequence alignment it is apparently shown the conserved sequence, conservative mutations semi-conservative mutation, and non-conservative mutations among nine different sequences.
Hence, this multiple alignment tool is fast and accurate tool for agriculture research. The results can be further Greek clados "branch" and gramma "character", is a map used in cladistics analysis which shows associations between organisms. A an evolutionary tree since it does not show how ancestors are related to offspring or how much they have distorted. Many evolutionary trees can be indirect from a particular cladogram. A cladogram uses lines that devise off in dissimilar directions ending at a clade, groups of organisms with a concluding common ancestor. There are many builds of cladograms but they all have lines that branch off from supplementary lines. The lines can be followed back to where they branch off. These ymbolize a hypothetical ancestor (not a genuine entity) which is inferred to display the traits shared between the concluding taxa above it. This hypothetical ancestor might then supply clues about the arrangement of evolution of diverse features, alteration, and other evolutionary narratives about ancestors. Even if conventionally such cladograms were generated mostly on the basis of morphological typescript, DNA and RNA sequencing data and computational phylogenetics are eration of cladograms, either on their own or in amalgamation with morphology We had concluded with above study that CLUSTAL O tool can be used for multiple sequence alignment for all nine model plants from different families and how we can generate phylogenetic tree from the same tool. With Fig 1  one

V. ACKNOWLEDGMENT
Authors are very grateful to Jacob School of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Deemed University, Allahabad