Abstract
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
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Copyright© 2018
Tabassum Khan Nida.
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This work is licensed under a Creative Commons Attribution 4.0 International License.
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.
Competing interests The authors have declared that no competing interests exist.
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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 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 Given below is a list of few bioinformatics tools used in genomics Bioinformatics plays an important role in comparative genomics by determing the genomic structural and functional relationship between different biological species Given below is a list of few bioinformatics tools used in comparative genomics 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 Given below is a list of few bioinformatics tools used in proteomics 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 Bioinformatic tools such as NCI 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 A number of databases consists of DNA profiles of known delinquents 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 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 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) Given below is a list of few bioinformatics tools used in gene expression study 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 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 Given below is a list of few bioinformatics tools used in protein structure and function prediction 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 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
Carrie
Transcriptional regulatory networks database
CisML
Motif detection tool
ICSF
Identification of conserved structural features in TF binding sites
Possum
Tool for motif searching
Promoser
Promoter extraction tool from eukaryotic organisms
REPFIND
Determine clustered repeats in DNA fragment
Cluster‐Buster
Tool for predicting motifs cluster in DNA sequences
Cister
Finds regulatory regions in DNA fragments
Clover
Find overrepresented motifs in DNA sequences
GLAM
Tool for predicting functional motifs
MotifViz
Identification of overrepresented motifs
RANKGENE
Tool for analysing gene expression data
ROVER
Predicts overrepresented motifs in DNA fragments
SeqVISTA
Sequences viewer tool
Tractor
Tool to find transcription factors with over‐represented binding sites in the upstream regions of co‐expressed human genes
OHMICS
Oral human microbiome integrated computational system
BLAST
DNA or protein sequence alignment tool
HMMER
Homologous protein sequences searching tool
Clustal Omega
Multiple sequence alignments tool
Sequerome
Sequence profiling tool
ProtParam
Predicts the physico-chemical properties of proteins
novoSNP
Predicts single point mutation in DNA sequences
ORF Finder
Find open reading frame in putative genes
Virtual Foorprint
Analysis of whole prokaryotic genome
WebGeSTer
Predicts gene termination sites during transcription
Genscan
Find exon-intron sites in DNA sequences
Softberry Tools
Genomes annotation tool along with the structure and function prediction of biological molecules
MEGA
Study evolutionary relationship
MOLPHY
Maximum likelihood based phylogenetic analysis tool
PHYLIP
Tool for phylogenetic studies
JStree
Tool for viewing and editing phylogenetic trees
Jalview
It is an alignment editing tool
DNA Data Bank of Japan
Resources for nucleotide sequences
Rfam
Database contains collection of RNA families
Uniprot
Protein sequence database
Protein Data Bank
Database provide data on structures of nucleic acids, proteins etc
SWISS PROT
Database containing the manually annotated protein sequences
InterPro
Provide information on protein families, its conserved domains and actives sites
Proteomics Identifications Database
Contains data on functional characterization and post-translation modification of proteins and peptides
Ensembl
Database containing annotated genomes of eukaryotes including human, mouse and other vertebrates
Medherb
Database for medicinally herbs
K2 / FAST
Protein structure alignment tool
SMM
Tool for determing peptides binding to major histocompatibility complex
ZDOCK
Protein‐protein docking tool
Docking Benchmark
Tool to evaluate docking algorithms performance
ZDOCK Server
An automated server for running ZDOCK
Z3OnWeb.com
Proteomic analysis for analysing 2D-Gel images
GeneChords
Conserved gene retrieval tool
GENEVA
Categorizes segmentally altered genes in many complete microbial genomes
HuGE Index
Human tissues gene expression database
Inverted Repeats Finder
Find inverted repeats in genomic DNA
ORChID
Database stores hydroxyl radical cleavage data of DNA sequences
Operons
Predicts functional gene clusters
Optimus
Retrieve conserved gene cluster data from numerous microbial genomes
Predictome
Visualizing tool for bio complexes
Tandem Repeat Database
Store information on tandem repeats in genomic DNA
VisANT
Tools for visualizing and analysing many biological interactions
BSG
Identification of transcription factor binding sites
TFSVM
Detection of transcription factor binding site
CATH
Tool for the categorized organization of proteins
Phyre and Phyre2
Tool for protein structure prediction
HMMSTR
For the prediction of sequence-structure correlations in proteins
MODELLER
Predicts 3D structure of protein
JPRED/ APSSP2
Predicts secondary structures of proteins
RaptorX
Predicts protein structure
PHD
Predicts neural network structure