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Saturday, 27 February 2021

Tools and Applications of bioinformatics in fisheries science | Bioinformatics and Aquaculture

 

Tools and Applications of bioinformatics in fisheries science


Introduction to Bioinformatics in fisheries

Fish Tools

By the term Bioinformatics, we mean the application of statistics and computer science to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatics processes in biotic systems. Bioinformatics can also be defined as a “science of solving biological problem using a mathematical and computational approach”.  Its primary use since the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing. Extending its application in the field of Fisheries sciences, bioinformatics can have following applications: Bioinformatics can be used in mapping and analyzing DNA and protein sequences of various fish species.  Further it can be put into use for aligning DNA and protein sequences of different fish species to compare them. Its applications extend into creating and viewing 3-D models of protein structures. By virtue of sequencing the genome of different fish species, we can search for specific genes and their functions. Fish populations can be made healthier, more disease-resistant and much more productive. Bioinformatics can help in drug development and discovery and thereby changing the state of fish populations.


Applications of Bioinformatics in Fisheries:

Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. The need for Bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal of this project - determination of the sequence of the entire human genome (approximately three billion base pairs) - will be reached by the year 2002.


Bioinformatics in fishries

 The science of Bioinformatics, which is the melding of molecular biology with computer science, is essential to the use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery. In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting of computational biologists and bioinformatics computer scientists. Such groups will be key to unraveling the mass of information generated by large scale sequencing efforts underway in laboratories around the world.

Molecular medicine requires the integration and analysis of genomic, molecular, cellular, as well as clinical data and it thus offers a remarkable set of challenges to bioinformatics. Bioinformatics nowadays has an essential role both, in deciphering genomic, transcriptomic, and proteomic data generated by high-throughput experimental technologies, and in organizing information gathered from traditional biology and medicine.

The evolution of bioinformatics, which started with sequence analysis and has led to high-throughput whole genome or transcriptome annotation today, is now going to be directed towards recently emerging areas of integrative and translational genomics, and ultimately personalized medicine. Therefore considerable efforts are required to provide the necessary infrastructure for high-performance computing, sophisticated algorithms, advanced data management capabilities, and-most importantly-well trained and educated personnel to design, maintain and use these environments. This review outlines the most promising trends in bioinformatics, which may play a major role in the pursuit of future biological discoveries and medical applications. Bioinformatics is a comparatively younger discipline that bridges the life sciences and computer sciences.

 The explosive growth of biological sequence information has made it imperative to integrate these two disciplines. Organization and analysis of biological data are the main activities of bioinformatics. Algorithms to create, maintain and access the sequence databases are among the most important contributions that bioinformatics has made for the life sciences. In the flow of genetic information from sequence to function, the stored information is translated twice: first from DNA to mRNA in the process of transcription, then from mRNA to protein in the process of translation. DNA and protein sequence comparisons have become routine steps in biochemical characterization, from newly cloned proteins to entire genomes. Genomics attempts to make a complete inventory of genes and nucleic acid sequences. In contrast to genomics approach, proteomics attempts to study the expressed proteins. Protein manifest physiological as well as pathophysiological processes in a cell or an organism and proteomics describe the complete inventory of proteins in dependence on in vivo parameters. Proteomics is complementing genomics as a tool to study life sciences.


The two key technologies in experimental proteomics are:

 1) 2-D PAGE with image analysis and

2) Biological mass spectrometry (MS) with database searching.

2-D PAGE technique is finding application in fisheries for identification of serum/plasma proteins that might be involved in the constitutive resistance to infections, muscle protein characterization, and biochemical analysis of cross-reactive antigens, understanding the molecular pathogenesis and genetics of disease resistance. We are developing 2D-refernce maps of commercially important fish and shellfish and plan to construct an index of the piscine proteins, by the construction of 2D-database that may be useful in identification of quantitative trait loci (QTL).


Bioinformatics tools

Bioinformatics tools

Bioinformatics Tools Bioinformatics Tools the Bioinformatics tools are the software programs for the saving, retrieving and analysis of Biological data and extracting the information from them. Factors that must be taken into consideration when designing these tools are: The end user (the biologist) may not be a frequent user of computer technology and thus it should be very user friendly. These software tools must be made available over the internet given the global distribution of the scientific research community


Types of bioinformatics tools

1. Homology and Similarity Tools

The term homology implies a common evolutionary relationship between two traits - whether they are DNA sequences or bristle patterns on a fly's nose. Homologous sequences are sequences that are related by divergence from a common ancestor. Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false. This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated.


2. Protein Function Analysis

Function Analysis is Identification and mapping of all functional elements (both coding and non-coding) in a genome. This group of programs allows you to compare your protein sequence to the secondary (or derived) protein databases that contain information on motifs, signatures and protein domains. Highly significant hits against these different pattern databases allow you to approximate the biochemical function of your query protein.


3. Structural Analysis

This set of tools allows you to compare structures with the known structure databases. The function of a protein is more directly a consequence of its structure rather than its sequence with structural homologs tending to share functions. The determination of a protein's 2D/3D structure is crucial in the study of its function


4. Sequence Analysis

This set of tools allows you to carry out further, more detailed analysis on your query sequence including evolutionary analysis, identification of mutations, hydropath regions and compositional biases. The identification of these and other biological properties are all clues that aid the search to elucidate the specific function of your sequence.


Important bioinformatics tools used infisheries and aquaculture

BLAST:

The Basic Local Alignment Search Tool (BLAST) for comparing gene and protein sequences against others in public databases, now comes in several types including PSI-BLAST, PHI-BLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences. Blast is an algorithm and programme for comparing primary biological sequence information such as amino acid sequence of proteins or nucleotides of DNA or RNA. BLAST can be used in the field of fisheries in several purposes, these include


1. Identifying different fish species:-

With the use of BLAST we can possibly correctly identify a species or find the homologous species. This can be useful for example when we are working with a DNA sequence from the unknown species.


2. DNA mapping of fishes:-

When working with known species and looking to sequence a gene at an unknown location, BLAST can compare the chromosomal position of sequence of interest to relevant sequence in data base.


3. Establishing phylogeny:-

Using the results received through the BLAST, we can create a phylogenetic tree using the BLAST web page.


4. Comparison of different fish species:-

When working with Gene’s, Blast can locate common genes in two related species and can be used to map annotations from one organism to another.


FASTA

A database search tool used to compare a nucleotide or peptide sequence to a sequence database. The program is based on the rapid sequence algorithm described by Lipmann and Pearson. It was the first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "in" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-top" variable which specifies the size of a "word".


EMBOSS

EMBOSS (The European Molecular Biology Open Software Suite) is a new, free open source software analysis package specially developed for the needs of the molecular biology user community. Within EMBOSS you will find around 100 programs (applications) for sequence alignment, database searching with sequence patterns, protein motif identification and domain analysis, nucleotide sequence pattern analysis, codon usage analysis for small genomes, and much more It stands for European Molecular Biology open software suite. It is a free open source software analysis package developed for the needs of molecular Biology and bioinformatics user community. It is used in the field of fisheries for following purposes:-

1. Sequence alignment.

2. Rapid data base searching with sequence patterns.

3. Protein identification including domain analysis.

4. Nucleotide sequence pattern analysis.

5. Codon usage analysis for small genomes.


Clustalw

ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences, calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.


RasMol

It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program.


Bioinformatics needs in the field of fisheries:-

As we know the Organization and analysis of biological data are the main activities of bioinformatics. In the flow of genetic information from sequence to function, the stored information is translated twice: first from DNA to mRNA in the process of transcription, then from mRNA to protein in the process of translation.  DNA and protein sequence comparisons have become routine steps in biochemical characterization, from newly cloned proteins to entire genomes. Genomics attempts to make a complete inventory of genes and nucleic acid sequences. In contrast to genomics approach, proteomics attempts to study the expressed proteins. Protein manifest physiological as well as pathophysiological processes in a cell or an organism and proteomics describe the complete inventory of proteins in dependence on in vivo parameters. Proteomics is complementing genomics as a tool to study life sciences.


Branches of applied bioinformatics

branches of bioinformatics s


1. Sequence analysis

2. Genome annotation

3. Computational evolutionary biology

4. Literature analysis

5. Analysis of gene expression

6. Analysis of regulation

7. Analysis of protein expression

8. Modeling biological systems

9. High-throughput image analysis

10. Molecular Interaction

11. Prediction of protein structure

 

Note: Our Next topic will be

Applied bioinformatics statistics and economics in fisheries research

Credit of Writing: Last year students of the Faculty of Fisheries- Kashmir: (Sabreena, Taranum, Sabiya, Asra, Ishrat, Arsh, Ambreen, Samreena, Mufassil, Midhat, Falak, Shahida, Uzma, Gowher, Sajad, Shahid, Ubaid and Wasim

 

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