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
Academic Editor: Hammad Afzal, SZABIST, Karachi.
Checked for plagiarism: Yes
Review by: Single-blind
Copyright © 2018 Nida Tabassum Khan
The authors have declared that no competing interests exist.
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:
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.Table 1. Bioinformatics tools/databases used in Genomics
|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 19, 20|
|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|
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.Table 2. Bioinformatics tools/databases used in Comparative genomics
|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 34, 35|
|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|
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 54, 55. 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.Table 3. Bioinformatics tools/databases used in Proteomics
|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|
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 62, 63.
Cancer Research and Analysis
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.
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.
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 74, 75.
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) 76, 77.
Given below is a list of few bioinformatics tools used in gene expression study Table 4.Table 4. Bioinformatics tools/databases used in Gene expression
|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|
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 90, 91.
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.Table 5. Bioinformatics tools/databases used in Protein structure and function prediction
|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|
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.
Thus bioinformatics holds significant importance in countless disciplines of biotechnology such as comparative genomics, drug designing, proteomics, molecular modelling, microbial genomics etc