Chapter 4 Tools used in sequence alignment
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Varruchi Sharma
Abstract
In ancient times, when the number of organisms in this world was comparatively on the lower side, the evolution between them could be easily described. But as newer organisms evolved, it became difficult to describe the evolutionary relationship between them. To solve this problem, a branch of science called bioinformatics emerged. Researchers developed a sequence alignment tool, which is a very important tool in today’s era. Sequence alignment is a fundamental technique in bioinformatics that has software programs to compare and align two or more biological sequences, such as DNA, RNA, or protein sequences. These tools help researchers identify conserved regions, functional domains, and evolutionary relationships among sequences. There are lots of sequence alignment tools like ClustalW, Muscle, MAFFT, T-Coffee, BLAST (Basic Local Alignment Search Tool), Needleman-Wunsch, and Smith-Waterman algorithm. They are used by researchers to provide fruitful information for new research. These tools typically accept input in various formats, such as FASTA or FASTQ, and provide output in the form of alignment files (e.g., Clustal format) or visual representations. The choice of alignment tool depends on the specific analysis requirements, the size of the dataset, and the desired level of accuracy. Researchers often use a combination of tools and visual inspection to validate and interpret the results of sequence alignments. The actual direction of sequence alignment tools will be influenced by ongoing research, technological advancements, and the specific needs of the scientific and medical communities.
Abstract
In ancient times, when the number of organisms in this world was comparatively on the lower side, the evolution between them could be easily described. But as newer organisms evolved, it became difficult to describe the evolutionary relationship between them. To solve this problem, a branch of science called bioinformatics emerged. Researchers developed a sequence alignment tool, which is a very important tool in today’s era. Sequence alignment is a fundamental technique in bioinformatics that has software programs to compare and align two or more biological sequences, such as DNA, RNA, or protein sequences. These tools help researchers identify conserved regions, functional domains, and evolutionary relationships among sequences. There are lots of sequence alignment tools like ClustalW, Muscle, MAFFT, T-Coffee, BLAST (Basic Local Alignment Search Tool), Needleman-Wunsch, and Smith-Waterman algorithm. They are used by researchers to provide fruitful information for new research. These tools typically accept input in various formats, such as FASTA or FASTQ, and provide output in the form of alignment files (e.g., Clustal format) or visual representations. The choice of alignment tool depends on the specific analysis requirements, the size of the dataset, and the desired level of accuracy. Researchers often use a combination of tools and visual inspection to validate and interpret the results of sequence alignments. The actual direction of sequence alignment tools will be influenced by ongoing research, technological advancements, and the specific needs of the scientific and medical communities.
Chapters in this book
- Frontmatter I
- Contents V
- Contributors VII
- Chapter 1 Introduction to bioinformatics 1
- Chapter 2 Biological databases and bioinformatics tools 13
- Chapter 3 Fundamentals of bioinformatics 41
- Chapter 4 Tools used in sequence alignment 61
- Chapter 5 Recent advances in the discovery of drug molecules: trends, scope, and relevance 83
- Chapter 6 Computer-aided drug design and drug discovery 103
- Chapter 7 Immunoinformatics: computational keys to immune system secrets 123
- Chapter 8 Phylogenetic analysis 141
- Chapter 9 Basic structure of proteins: current paradigms, trends, and perspective 151
- Index 171
Chapters in this book
- Frontmatter I
- Contents V
- Contributors VII
- Chapter 1 Introduction to bioinformatics 1
- Chapter 2 Biological databases and bioinformatics tools 13
- Chapter 3 Fundamentals of bioinformatics 41
- Chapter 4 Tools used in sequence alignment 61
- Chapter 5 Recent advances in the discovery of drug molecules: trends, scope, and relevance 83
- Chapter 6 Computer-aided drug design and drug discovery 103
- Chapter 7 Immunoinformatics: computational keys to immune system secrets 123
- Chapter 8 Phylogenetic analysis 141
- Chapter 9 Basic structure of proteins: current paradigms, trends, and perspective 151
- Index 171
