Advances in Bioinformatics

446 Pages·2021·9.424 MB·English

by  Vijai Singh, Ajay Kumar

Vijai Singh
Ajay Kumar   Editors
Advances in
Bioinformatics
Advances in Bioinformatics
(cid:129)
Vijai Singh Ajay Kumar
Editors
Advances in
Bioinformatics
Editors
VijaiSingh AjayKumar
DepartmentofBiosciences Biotechnology
IndrashilUniversity RamaUniversity
Mehsana,Gujarat,India Kanpur,UttarPradesh,India
ISBN978-981-33-6190-4 ISBN978-981-33-6191-1 (eBook)
https://doi.org/10.1007/978-981-33-6191-1
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Foreword
IamhappytowritetheforewordtotheAdvancesinBioinformatics,atimelyvolume
ontherapidlygrowingfield.
Bioinformatics was born when biological data was generated in numbers that
necessitated its management mainly in terms of storage, analysis, output, and
communication. To begin with, bioinformatics had to mainly deal with protein
structurestudies.Overtime,therehasbeenasurgeofdata,frompartstopathways
tomulticellularcontexts.Databaseshavebecomethenorminbiologyandmodeling
hasmadesignificantinroadsintotheexperimentallabs.
Thisbookcoversbasicandadvancedaspectsofbioinformaticsintermsoftools,
datamining,analytics,computationalevolutionarybiology,computationalvaccine,
and drug design. It also covers proteomics, metabolomics, DNA sequencing and
NGStogenomeanalysis,biologicalcomputation,neuralnetworkanalysis,bigdata
analysis, soft computing, and artificial intelligence. All chapters are written by
eminentscientistswhohavewell-establishedresearchinbioinformatics.
I am delighted to observe the valuable efforts of Dr. Vijai Singh and Dr. Ajay
Kumar,whohaveworkedhardtobringoutanexcellentvolumewiththesupportof
SpringerNature.
This book offers a valuable source of information for not only beginners in
bioinformaticsbutalsoforstudents,researchers,scientists,clinicians,practitioners,
policymakers, stakeholders who are interested in harnessing the potential of bioin-
formaticsfromfundamentalsciencetoapplications.
SchoolofBiotechnology, PawanK.Dhar
JawaharlalNehruUniversity,
NewDelhi,India
vv
Preface
Bioinformatics is a rapidly growing area of biology and has gained significant
scientific and public attention. It is currently used in all domains of biological
sciences research and has accelerated the research work. It combines principles of
biology, computer science, information technology, mathematics, and statistics to
analyze and interpret biological data. This book covers the momentousness of
bioinformatics assistance and knowledge, thereby highlighting its role in the
advancement of modern science. It plays major roles in the development of
biological science, without which the researchers’ community cannot extricate,
assess,oranalyzeanytypeoflarge-scaleparadigmwhetheritisgenomics,proteo-
mics,ortranscriptomicswhichensurestotacklebiologicalproblems.
Awiderangeoftopicsfrombasictoadvancedlevelofbioinformaticshavebeen
covered. This book covers introduction, tools, data mining and analysis, computa-
tional evolutionary biology, protein analysis, computational vaccine, and drug
design. It also covers computational genomics, proteomics, metabolomics, DNA
sequencingandNGS,microRNA,genetogenomeanalysis,biologicalcomputation,
neuralnetworkanalysis,artificialintelligence,bigdataanalysis,softcomputing,and
manyotherrelevanttopics.
We believe that this book covers great range of topic in different aspects of
bioinformatics.Thisbookoffersanexcellentandinformativetextonbioinformatics,
benefitted by simple to understand and easy to read format. This book uses a rich
literary text of excellent depth, clarity, and coverage. It highlights a number of
aspects of bioinformatics in a way that can help future investigators, researchers,
students, and stakeholders to perform their research with greater ease. This book
providesan excellent basis from which scientific knowledge cangrow,widen, and
acceleratebioinformaticsresearchinmanyareas.
Mehsana,Gujarat,India VijaiSingh
Kanpur,UttarPradesh,India AjayKumar
vii
Acknowledgement
IwouldliketoexpressmysinceregratitudeanddeepappreciationtoDr.J.S.Yadav,
Director(Research),IndrashilUniversity,India,for extendinghisoutstandingsup-
port and motivation to complete this book. I would like to give many thanks to
co-editorDr.AjayKumarSinghofthisbookwhogavemeoutstandingpersonaland
professionalsupportaswellasinspirationtofinishthisbook.
I am delighted to thank all the authors for their excellent contributions to this
book.IwouldliketothankDr.BhavikSawhney(AssociateEditor—Biomedicine)
and Ms. Veena Perumal (Production Editor) from Springer for their excellent
managementofthisproject.
I would like to give thank Prof. Chaitanya G. Joshi, Prof. Rakesh Rawal, Prof.
Bharat Maitreya. Prof. Pawan K. Dhar, Dr. Poonam Bhargava, Dr. Madhvi Joshi,
Prof. S. R. Dave, Dr. Bhabatosh Das, Dr. Pablo Carbonell, Dr. Javin P. Oza, Dr.
RupeshMaurya,Dr.ShamsYazdani,Dr.IndraMani,Dr.SatyaPrakash,Dr.Vimal
C.Pandey,Dr.DinhToiChu,Dr.SureshRamakrishna,Dr.Prof.NisheethAgrawal,
andthosewhosenamesdonotfeatureherebuthavedirectlyorindirectlycontributed
in shaping this project. I greatly appreciate the support of my students Mr. Nisarg
Gohil,Mr.KhushalKhambhati,andMs.GargiBhattacharjee,whosediscussionand
commentshelpedtoshapethisbook.
I wish to express my gratitude to my beloved wife Pritee Singh for her endless
support,patience,andinspiration.LotsofaffectionformykidsAaradhyaandAyush
whomissedmeduringthisproject.Iwouldliketowarmlythankthefacultyandstaff
ofIndrashilUniversityforprovidingagreatworkingenvironment.
Iamawarethatevendespiteourbestefforts,thefirstversionalwayscomeswith
some error that may have crept inthe compilation.Iwouldbe delighted toreceive
feedback from readers to further improve the future book. Last but not least, my
sincere thanks to GOD for his supreme POWER for endowingme to live with joy
andvictoryintheshapeofthisbook.
VijaiSingh
This book is an outcome of utter studies and literature survey. I express my
profoundgratitudetofamily,friends,andcolleagueswhoalwayshavegoodwords
formeinculcatingasourceofstrengthandinspirationfortakingthisventure.
ix
x Acknowledgement
IamespeciallygratefultoDr.PrateekSingh(Director,RamaUniversityKanpur,
India), Dr. Pranav Singh (Director PR, Rama University), Dr. Hari Om Sharan
(Dean, Rama University), and Dr. Sandeep Shukla (Deputy Registrar, Rama Uni-
versity) who never stopped me to take this challenge for developing ideas and
supportedmetodevelopastrongfoundation.
I also take this opportunity to thank my worthy and learned colleagues in the
Department of Biotechnology, Faculty of Engineering and Technology, Rama
University, whose knowledge and experience have eased and developed the confi-
dencetotakeupmyworkandfinallytakingtofinishthenote.
I would also like to mention sincere cooperation from Er. Monisa Anwer and
Er. Fariya Khan, who always extended their helping hands for discussions and
cooperation.Andlastbutnotleast,Ifeeldeeplyandhighlyobligedtomybeloved
wife Shraddha and my children Nishit and Anshika who not only motivated meto
authorthisbookbutalsoshowedpatiencewhendeprivedthemofmymuch-needed
attentionduringthiscourseoftimesothatmybookcouldseethelightoftheday.It
wouldnotbeoutofplacetoseektheblessingsofmyelderbrotherEr.PremChandra
whoalwayshadbeenaguidingfigureinmypassion.
I am also thankful to Almighty God who has given me the wisdom to edit this
book. Finally, I dedicate this book to my parents for their countless blessings to
accomplishthetarget.
AjayKumar
Contents
1 AnIntroductionandApplicationsofBioinformatics. . . . . . . . . . . . 1
HennyPatel,DhrutiBhatt,ShreyaShakhreliya,NavyaL.Lam,
RupeshMaurya,andVijaiSingh
2 BioinformaticsToolsandSoftware. . . . . . . . . . . . . . . . . . . . . . . . . 15
AeshnaGupta,DishaGangotia,andIndraMani
3 RoleofBioinformaticsinBiologicalSciences. . . . . . . . . . . . . . . . . . 37
DishaGangotia,AeshnaGupta,andIndraMani
4 ProteinAnalysis:FromSequencetoStructure. . . . . . . . . . . . . . . . 59
JaykumarJaniandAnjuPappachan
5 ComputationalEvolutionaryBiology. . . . . . . . . . . . . . . . . . . . . . . 83
SubhamoyBanerjee
6 Web-BasedBioinformaticsApproachTowardsAnalysis
ofRegulatorySequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
B.SharanSharma,SonalR.Bakshi,PreetiSharma,
andRamtejJ.Verma
7 AnOverviewofBioinformaticsResourcesforSNPAnalysis. . . . . . 113
SudarkodiSukumar,ArunikaKrishnan,andSubhamoyBanerjee
8 VaccineDesignandImmunoinformatics. . . . . . . . . . . . . . . . . . . . . 137
FariyaKhanandAjayKumar
9 Computer-AidedDrugDesigning. . . . . . . . . . . . . . . . . . . . . . . . . . 151
ThakorRajkishan,AilaniRachana,SuraniShruti,PatelBhumi,
andDhavalPatel
10 ChemoinformaticsandQSAR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
VivekSrivastava,ChandraboseSelvaraj,andSanjeevKumarSingh
xxii
xii Contents
11 ComputationalGenomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
FabrícioAlmeidaAraújo,AnaLidiaQueirozCavalcante,
MarcusdeBarrosBraga,RodrigoBentesKato,
RommelThiagoJucáRamos,
andEdianFranklinFrancoDeLosSantos
12 AGuidetoRNAseqDataAnalysisUsingBioinformatics
Approaches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
PreetiSharma,B.SharanSharma,andRamtejJ.Verma
13 ComputationalMetabolomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
PriyaRanjanKumar,SantoshKumarMishra,andSarikaSrivastava
14 NextGenerationSequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
AnchitaPrasad,HarshitaBhargava,AyamGupta,
NidhiShukla,ShaliniRajagopal,SonalGupta,AmitaSharma,
JayaramanValadi,VinodNigam,andPrashanthSuravajhala
15 BioinformaticsinPersonalizedMedicine. . . . . . . . . . . . . . . . . . . . . 303
G.SunilKrishnan,AmitJoshi,andVikasKaushik
16 BioinformaticsToolsforGeneandGenomeAnnotation
AnalysisofMicrobesforSyntheticBiologyandCancer
BiologyApplications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
EkeneEmmanuelNweke,EssaSuleman,MorneDuPlessis,
andDeepakB.ThimiriGovindaRaj
17 BioinformaticsforHumanMicrobiome. . . . . . . . . . . . . . . . . . . . . . 333
AbhirupaGhosh,ShaziaFirdous,andSudiptoSaha
18 NeuralNetworkAnalysis. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. 351
AmitJoshi,JitendraSasumana,NillohitMitraRay,
andVikasKaushik
19 RoleofBioinformaticsinMicroRNAAnalysis. . . . . . . . . . . . . . . . 365
IndraMani
20 BioinformaticsforImageProcessing. . . . . . . . . . . . . . . . . . . . . . . . 375
DilipKumarJ.SainiandDhirendraSiddharth
21 ArtificialIntelligenceinBioinformatics. . . . . . . . . . . . . . . . . . . . . . 395
HariOmSharan
22 BigDataAnalysisinBioinformatics. . . . . . . . . . . . . . . . . . . . . . . . 405
AnugrahSrivastavaandAdvaitNaik
23 SoftComputinginBioinformatics. . . . . . . . . . . . . . . . . . . . . . . . . . 431
VivekSrivastava