JBBS Journal of Biotechnology and Biomedical Science 2576-6694 Open Access Pub United States JBBS-18-2173 10.14302/issn.2576-6694.jbbs-18-2173 review-article The Emerging Role of Bioinformatics in Biotechnology Nida Tabassum Khan 1 * Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology Engineering and Management Sciences,(BUITEMS),Quetta, Pakistan corresponding author Hammad Afzal 1 SZABIST, Karachi. Nida Tabassum Khan, Department of Biotechnology, Faculty of Life Sciences, and Informatics,, Balochistan, University of Information Technology Engineering and Management Sciences,(BUITEMS),Quetta, Pakistan, . Email: nidatabassumkhan@yahoo.com

The authors have declared that no competing interests exist.

 07 08 2018 1 3 13 24 18 06 2018 02 08 2018 07 08 2018 © 2018 Nida Tabassum Khan This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This article is available from http://openaccesspub.org/jbbs/article/803

Bioinformatic tools is widely used to manage the enormous genomic and proteomic data involving DNA/protein sequences management, drug designing, homology modelling, motif/domain prediction ,docking, annotation and dynamic simulation etc. Bioinformatics offers a wide range of applications in numerous disciplines such as genomics. Proteomics, comparative genomics, nutrigenomics, microbial genome, biodefense, forensics etc. Thus it offers promising future to accelerate scientific research in biotechnology

CisML Possum Clover SeqVISTA WebGeSTer GeneChords. Introduction

Bioinformatics provided computational ways for data analysis by employing informatics tools and softwares to determine protein/gene structure or sequence, homology, molecular modeling of biological system, molecular docking etc to analyze and interpret data in insilico 1.Currently bioinformatics have become a principal technology in all life sciences research. Bioinformatics has been integrated into a number of different disciplines where it assists in better understanding of the data in a shorter time frame 2. With the massive advancement in information technology, bioinformatics is growing rapidly providing new ways and approaches for the assessment of valuable data 3.Data mining and manipulations is an important aspect of bioinformatic 4. It allows researchers to collect, store, catalogue and analyse information in unique format that is easily manipulated for future research 5. Some examples of data manipulation include molecular online tools and the bio extract server 6. It is useful for accessing bimolecular data from many sources for many purposes. This is lab template for the proper accession and usage of online molecular tools like bio extract 7.

Some applications of bioinformatics in biotechnology is given below:

Genomics

To manage an escalating amount of genomic information, bioinformatic tools are required to maintain and analyze the DNA sequences from different organism 8. Determination of sequence homology, gene finding, coding region identification, structural and functional analyses of genomic sequences etc, all this is possible by the use of different bioinformatics tools and software packages 9.

Given below is a list of few bioinformatics tools used in genomics Table 1.

Bioinformatics tools/databases used in Genomics
Bioinformatics tools Purpose
Carrie Transcriptional regulatory networks database 10
CisML Motif detection tool 11
ICSF Identification of conserved structural features in TF binding sites 12
Possum  Tool for motif searching 13
Promoser Promoter extraction tool from eukaryotic organisms 14
REPFIND Determine clustered repeats in DNA fragment 15
Cluster‐Buster Tool for predicting motifs cluster in DNA sequences 16
Cister Finds regulatory regions in DNA fragments 17
Clover Find overrepresented motifs in DNA sequences 18
GLAM Tool for predicting functional motifs 1920
MotifViz Identification of overrepresented motifs 21
RANKGENE Tool for analysing gene expression data 22
ROVER Predicts overrepresented motifs in DNA fragments 23
SeqVISTA Sequences viewer tool 24
Tractor Tool to find transcription factors with over‐represented binding sites in the upstream regions of co‐expressed human genes 25
OHMICS Oral human microbiome integrated computational system 26
Comparative Genomics

Bioinformatics plays an important role in comparative genomics by determing the genomic structural and functional relationship between different biological species 27.

Given below is a list of few bioinformatics tools used in comparative genomics Table 2.

Bioinformatics tools/databases used in Comparative genomics
Bioinformatics tools Purpose
BLAST DNA or protein sequence alignment tool 28
HMMER Homologous protein sequences searching tool 29
Clustal Omega Multiple sequence alignments tool 30
Sequerome Sequence profiling tool 31
ProtParam Predicts the physico-chemical properties of proteins 32
novoSNP Predicts single point mutation in DNA sequences 33
ORF Finder Find open reading frame in putative genes 3435
Virtual Foorprint Analysis of whole prokaryotic genome 36
WebGeSTer Predicts gene termination sites during transcription 37
Genscan Find exon-intron sites in DNA sequences 38
Softberry Tools Genomes annotation tool along with the structure and function prediction of biological molecules 39
MEGA Study evolutionary relationship 40
MOLPHY Maximum likelihood based phylogenetic analysis tool 41
PHYLIP Tool for phylogenetic studies 42
JStree Tool for viewing and editing phylogenetic trees 43
Jalview It is an alignment editing tool 44
DNA Data Bank of Japan Resources for nucleotide sequences 45
Rfam Database contains collection of RNA families 46
Uniprot Protein sequence database47
Protein Data Bank Database provide data on structures of nucleic acids, proteins etc 48
SWISS PROT Database containing the manually annotated protein sequences 49
InterPro Provide information on protein families, its conserved domains and actives sites 50
Proteomics Identifications Database Contains data on functional characterization and post-translation modification of proteins and peptides 51
Ensembl Database containing annotated genomes of eukaryotes including human, mouse and other vertebrates 52
Medherb Database for medicinally herbs 53
Proteomics:

Advanced molecular based techniques led to the accumulation of huge proteomic data of protein activity patterns, interactions, profiling, composition, structural information, image analysis, peptide mass fingerprinting, peptide fragmentation fingerprinting etc 5455. This enormous data could be managed by using different tools of bioinformatics.

Given below is a list of few bioinformatics tools used in proteomics Table 3.

Bioinformatics tools/databases used in Proteomics
Bioinformatics tools Purpose
K2 / FAST Protein structure alignment tool 56
SMM Tool for determing peptides binding to major histocompatibility complex 57
ZDOCK Protein‐protein docking tool 58
Docking Benchmark Tool to evaluate docking algorithms performance 59
ZDOCK Server An automated server for running ZDOCK 60
Z3OnWeb.com Proteomic analysis for analysing 2D-Gel images 61
Drug Discovery

Clinical bioinformatics is an emerging new field of bioinformatics that employs various bioinformatics tool such as computer aided drug designing to design novel drugs, vaccines, DNA drug modelling ,insilico drug testing,etc to produce new and effective drugs in a shorter time frame with lower risks 6263.

 Cancer Research and Analysis

Bioinformatic tools such as NCI 64, NCIP (part of NCI) 65 and CBIIT 66 have played an important role in genomics, proteomics, imaging, and metabolomics to increase our knowledge of the molecular basis of cancer 67.

 Phylogenetic Studies

Using numerous bioinformatics tools, phylogenetic analysis of the molecular data can easily be achieved in a short period of time by constructing phylogenetic trees to study its evolutionary relationship based on sequence alignment 68.

 Forensic Science

A number of databases consists of DNA profiles of known delinquents 69. Advancement in microarray technology, bayesian networks, programming algorithms etc provides an effective method of evidence organization and interpretation 7071.

 Bio-Defense

Though bioinformatics has limited impact on forensic since there is a need for more advanced algorithms and computational applications so that the established databases may exhibit interoperability with each other 72.

 Nutrigenomics

Progressions in structural /functional genomics and molecular technologies such as genome sequencing and DNA microarrays generates valuable knowledge which explains nutrition in relation of an individual’s genetics which directly influences its metabolism 73. Because of the influx of bioinformatics tools, nutrition-related research is tremendously increased 7475.

 Gene Expression

Regulation of gene expression is the core of functional genomics allowing researchers to apply genomic data to molecular technologies that can quantify the amount of actively transcribing genes in any cell at any time (e.g. gene expression arrays) 7677.

Given below is a list of few bioinformatics tools used in gene expression study Table 4.

Bioinformatics tools/databases used in Gene expression
Bioinformatics tools Purpose
GeneChords  Conserved gene retrieval tool 78
GENEVA Categorizes segmentally altered genes in many complete microbial genomes 79
HuGE Index Human tissues gene expression database 80
Inverted Repeats Finder Find inverted repeats in genomic DNA 81
ORChID Database stores hydroxyl radical cleavage data of DNA sequences 82
Operons Predicts functional gene clusters 83
Optimus Retrieve conserved gene cluster data from numerous microbial genomes 84
Predictome Visualizing tool for bio complexes 85
Tandem Repeat Database Store information on tandem repeats in genomic DNA 86
VisANT Tools for visualizing and analysing many biological interactions 87
BSG Identification of transcription factor binding sites 88
TFSVM Detection of transcription factor binding site 89
Food Quality

New improvements in computing algorithms and available structural simulation databases of recognized structures has brought molecular modeling into conventional food chemistry. Such simulations will make it possible to improve food quality by developing new food additives by comprehending the basis of taste tenacity, antagonism and complementation 9091.

Predicting Protein Structure and Function

Protein topology prediction is now so much easy thanks to bioinformatics which helps in the prediction of 3D structure of a protein to gain an insight into its function as well 92.

Given below is a list of few bioinformatics tools used in protein structure and function prediction Table 5.

Bioinformatics tools/databases used in Protein structure and function prediction
Bioinformatics tools Purpose
CATH Tool for the categorized organization of proteins 93
Phyre and Phyre2 Tool for protein structure prediction 94
HMMSTR For the prediction of sequence-structure correlations in proteins 95
MODELLER Predicts 3D structure of protein 96
JPRED/ APSSP2 Predicts secondary structures of proteins 97
RaptorX Predicts protein structure 98
PHD Predicts neural network structure 99
Personalized Medicine

Doctors will be able to analyse a patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning by employing bioinformatics tool 100.

Microbial Genome Applications

Microbes have been studied at very basic level with the help of bioinformatics tools required to analyse their unique set of genes that enables them to survive under unfavourable conditions 101.

Conclusion

Thus bioinformatics holds significant importance in countless disciplines of biotechnology such as comparative genomics, drug designing, proteomics, molecular modelling, microbial genomics etc

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