The National Center for Biotechnology Information (NCBI, 2001) defines bioinformatics as the field of science in which biology, computer science, and information technology merge into a single discipline. Fredj Tekaia defines Bioinformatics the mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information. Bioinformatics has emerged as an essential field of science that is facilitating biological discoveries since more than a decade. Without the usage of bioinformatics tools it is merely impossible to capture, manage process, analyse and interpret the huge amounts data that is available especially after whole genome sequencing projects. The sequencing of the genomes of plants and animals will have enormous benefits for the agricultural community. Bioinformatics tools can be used to search for the genes within these genomes and to elucidate their functions. This specific genetic knowledge could then be used to produce stronger, drought, disease and insect resistant crops and improve the quality. In agriculture it helps in the insect resistance, improve nutritional quality, rational plant improvement, waste cleanup, climate change studies, and development of drought resistance varieties (Dahiya and Lata, 2017) and in addition to this it also plays an important roles in biotechnology, antibiotic resistance, and forensic analysis of microbes, comparative studies, evolutionary studies and veterinary Sciences. Seri bioinformatics tools and techniques not only facilitated detection of proteomic and genomic diversity among the species/strains, but also resulted in finding a gap in the silkworm genome sequence of a strain that diverged during the course of domestication. Seri-bioinformatics databases are a valuable seri-bioresource. The available online resources on silkworm and its related organisms, including databases as well as informative websites help to make silkworms healthier, more disease resistant and more productive. These databases provides information on gene, protein sequences and diseases and play crucial roles in conservation of the silkworm species and mulberry plants (Singh et al., 216). Bioinformatics approaches give an insight, uncovering the lineage with gene and protein count of B. mori and Drosophila encompass ~18,000 and ~16,000 (Genes) and ~9,000 and ~22,000 (Proteins) respectively (Somshekar and Borgowda, 2013).

1. Bioinformatics and its applications in
agriculture/Sericulture

2. TEMPERATE SERICULTURAL RESEARCH
INSTITUTE MIRGUND
Seminar Title
Bioinformatics and its applications in agriculture/Sericulture
Credit Seminar By
Mohd Younus Wani
(Student of Ph.D. Sericulture)
Reg.No.2017-729-D
Seminar Incharge
Dr.M.F.Baqual
(Associate Professor,TSRI, Mirgund SKUAST-K.)
2

3. Bioinformatics
Term Bioinformatics was coined by Paulien Hogeweg and Ben
Hesper in 1970 as the study of informatic processes in biotic
systems.
Bioinformatics deals with computational management and
analysis of biological information (genes, genomes, proteins,
cells, ecological systems, medical information, robots, artificial
intelligence etc.
3

4. The National Center for Biotechnology
Information (NCBI 2001)
Bioinformatics as the field of science in which biology,
computer science, and information technology merge into a
single discipline.
Fredj Tekaia at the Institute Pasteur defines bioinformatics:
The mathematical, statistical and computing methods that aim
to solve biological problems using DNA and amino acid
sequences and related information.
4

5. Why is bioinformatics important
Bioinformatics has developed out of the need to understand
the code of life (DNA).
Massive DNA sequencing projects have evolved and added
in the growth of the science of bioinformatics.
The ultimate goal of bioinformatics is to uncover the wealth
of biological information hidden in the mass of sequence,
structure, literature and other biological data.
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6. Components of Bioinformatics
Technology Database Algorithm
Analysis
tools
Computing
power
6

7. Molecular Biology Computational Biology
GenomicsComputer Science
Bioinformatics
7

8. Bioinformatics brings together
Large data bases
of biological
information
Computational
techniques of
analysis
Life
8

9. What is done in bioinformatics
The development of new algorithms and statistics with which to assess
relationships among members of large data sets.
The analysis and interpretation of various types of data including
nucleotide and amino acid sequences, protein domains, and protein
structures.
The development and implementation of tools that enable efficient access
and management of different types of information.
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10. How do we use Bioinformatics?
Compile/distribute data for other researchers
Compare data with other researchers
Search for previously known functions of a gene
Predict function of unknown genes/proteins
Retrieve/compare gene sequences
Store/retrieve biological information (databases)
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11. SOFTWARE AND TOOLS
Software tools for bioinformatics range from simple command-line tools,
to more complex graphical programs.
The computational biological tool BLAST
An algorithm for determining the similarity of arbitrary sequences against
other sequences.
BLAST is one of the available programme for doing sequence alignment.
11

12. BLAST
Basic Local Alignment Search Tool.
It is an algorithm for comparing biological sequences information, such as amino acid sequence of
different proteins or the nucleotides of DNA sequences.
BLAST is used to identify library sequences that resembles the query sequences.
The BLAST program was designed by Eugene Myers, Stephen Altschul, Warren Gish, David J. Lipman
and Webb Miller at the NIH and was published in J. Mol. Biol. in 1990.
BLAST is a tool for alignment of sequences.
Link: http://www.ncbi.nlm.nih.gov/BLAST/
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13. 13

14. USES OF BLAST
Identifying Species
Locating Domains
Establishing Phylogeny
DNA Mapping
Comparison
14

15. Proteome and Proteomics
The terms proteome and proteomics were coined by Mark Wilkins
and colleagues in the early 1990
Proteome
It is the complement protein found in a single cell in a particular
environment.
It is complete collection of proteins encoded by genome of an
organism.
Proteomics
It is the study of composition, structure, function and interaction
of the proteins directing the activities of each living cell
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16. 16
Central dogma of molecular biology

17. Tools of proteomics
protein
Peptide mixture peptides
MS analysis
MS dataIdentification
separation
Protein mixture
digestion digestion
separation
Database search
Algorithms
17

18. Components of Expressional Proteomics
Protein
Separation
Mass
Spectroscopy
Bioinformatics
18

19. Applications of Proteomics
Post-Translational
Modifications
Protein-
Protein
Interaction
Molecular
Medicine
Protein
Expression
Profiling
19

20. Human Genome Project
Genomics is a new term describing the study of all genes of an
organism and their interactions with each other and with the
environment
Purpose: map the entire human genome
Complete sequencing of human genome completed 2003.
The Human Genome of one person fits on a flash drive
Began 1990
20

21. Life Science Vs Computer Science
Scientific algorithms made it possible to put together a
vast amount of data from sequencing machines when
the human genome was sequenced.
Computer science’s computational paradigm has shaped
new modes of inquiry in life sciences
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22. DNA?
22

23. Genes?
23

24. Protein Sequence?
24

25. Structure?
25

26. Expression?
26

28. Insect resistance
Genes from Bacillus thuringiensis that can control a
number of serious pests have been successfully
transferred to cotton, maize and potatoes.
This new ability of the plants to resist insect attack means
that the amount of insecticides being used can be reduced
and hence nutritional quality of the crops is increased.
28

29. Improve nutritional quality
Scientists have recently succeeded in transferring
genes into rice to increase levels of vitamin A, iron
and other micronutrients. This reduces the rate of
blindness from the world by giving genetically
modified rice to people.
29

30. Development of Drought resistance varieties
Progress has been made in developing cereal varieties
that have a greater tolerance for soil alkalinity, free
aluminium and iron toxicities. These varieties will
allow agriculture to succeed in poorer soil areas, thus
adding more land to the global production base.
Research is also in progress to produce crop varieties
capable of tolerating reduced water conditions.
30

31. Climate change Studies
Increasing levels of carbon dioxide
emission are thought to contribute to
global climate change. One way to
decrease atmospheric carbon dioxide
is to study the genomes of microbes
that use carbon dioxide as their sole
carbon source.
31

32. Alternative energy sources
Scientists are studying the genome
of the microbe Chlorobium tepidum
which has an unusual capacity for
generating energy from light.
32

33. Crop improvement
Genome sequencing of several important plants
species has enabled researchers to identify
‘chromosome’ and ‘difference’ factor in
sequences. This in turn has been used to identify
value traits for crop improvement.
For instance, the barley stem rust resistance gene
has been identified from rice-barley comparisons
and the sugarcane rust resistance gene based on
maize-sorghum comparisons.
At present the complete genomes of Arabidopsis
thaliana (water cress) and Oryza sativa (rice) are
available.
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34. 34

35. Veterinary Science
Sequencing projects of many farm animals
including cows and sheep are now well under way
in the hope that a better understanding of the
biology of these organisms will have huge impacts
for improving the production and health of
livestock and ultimately have benefits for human
nutrition.
35

36. Evolutionary studies
The sequencing of genomes from all three
domains of life, eukaryote, bacteria and
archaea means that evolutionary studies
can be performed in a quest to determine
the tree of life and the last universal
common ancestor.
36

37. Microbial genome applications
37
Microorganisms are ubiquitous, that is they are found everywhere. They have
been found surviving and thriving in extremes of heat, cold, radiation, salt,
acidity and pressure.
By studying the genetic material of these organisms, scientists can begin to
understand these microbes at a very fundamental level and isolate the genes
that give them their unique abilities to survive under extreme conditions.

38. Waste cleanup
Deinococcus radiodurans is known as the world's toughest
bacteria and it is the most radiation resistant organism
known.
Scientists are interested in this organism because of its potential
usefulness in cleaning up waste sites that contain radiation and toxic
chemicals.
38

39. Gene therapy
In the not too distant future, the potential
for using genes themselves to treat disease
may become a reality.
Gene therapy is the approach used to treat,
cure or even prevent disease by changing
the expression of a persons genes.
Currently, this field is in its infantile stage
with clinical trials for many different types
of cancer and other diseases ongoing.
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40. Forensic analysis of microbes
Scientists used their genomic tools to
distinguish between the strains of Bacillus
anthraces that was used in the summer of
2001 terrorist attack in Florida with that of
closely related anthrax strains.
40

41. The reality of bio-weapon creation
Scientists have recently built the virus poliomyelitis
using entirely artificial means. They did this using
genomic data available on the Internet and materials
from a mail-order chemical supply.
The research was financed by the US Department of
Defense as part of a bio-warfare response program
to prove to the world the reality of bio-weapons.
41

42. Antibiotic resistance
Scientists have been examining the genome of
Enterococcus faecalis a leading cause of bacterial
infection among hospital patients.
Anti biotic resistant genes that may contribute to the
bacterium's transformation from pathogenic to non
pathogen.
42

43. Drug development
At present all drugs on the market target only about 500
proteins. With an improved understanding of disease
mechanisms and using computational tools to identify and
validate new drug targets, more specific medicines that act
on the cause, not merely the symptoms of the disease can
be developed.
These highly specific drugs promise to have fewer side
effects than many of today's medicines.
43

44. Preventative medicine
With help of genetic mechanisms the development of diagnostic tests
to measure a person’s susceptibility to different diseases may become
a distinct reality.
Preventative actions such as change of lifestyle or having treatment at
the earliest possible stages will help to conquer the disease.
44

45. Molecular medicine
Every disease has a genetic component.
3000-4000 hereditary disease including Cystic Fibrosis and
Huntingtons disease) or a result of the body's response to an
environmental stress which causes alterations in the genome
(e.g. cancers, heart disease, diabetes).
Search for the genes directly associated with different diseases
and begin to understand the molecular basis of these diseases
more clearly. This new knowledge of the molecular mechanisms
of disease will enable better treatments, cures and even
preventative tests to be developed.
45

46. Biotechnology
Bacterium Thermotoga maritima have potential for practical applications
in industry and government-funded environmental remediation.
Corynebacterium glutamicum which is of high industrial interest as a
research object because it is used by the chemical industry for the
biotechnological production of the amino acid lysine.
Lactococcus lactis is one of the most important micro-organisms involved in the dairy
industry, it is a non-pathogenic rod-shaped bacterium that is critical for manufacturing
dairy products like buttermilk, yogurt and cheese. This bacterium is also used to prepare
pickled vegetables, beer, wine, some breads and sausages and other fermented foods.
46

48. Bioinformatics centre
The Bioinformatics centre at Central Sericultural
Research and Training Institute(CSRTI), Mysore was
established as a sub node of the BTISnet in 1999
primarily to support the biotechnological research in
sericulture.
48

49. Objectives of Seri bioinformatics
Maintain information repository of silkworm and mulberry
genotypes and breeds.
Develop and maintain the databases related to mulberry and
silkworm genomes with structural information.
To conduct training/workshops to create awareness and in sight in the
field of Bioinformatics in general and Seri-bioinformatics in
particular.
To provide online support information in the field of sericulture.
49

50. First Transgenic mulberry by Paramjit Khurana
Mulberry is adversely affected by stresses like salinity and drought (Lal et al. 2006).
India has developed the first transgenic mulberry plant in the world with drought and salinity tolerance.
The breakthrough was achieved in a laboratory in South Campus, Delhi University, where the transgenic plants are
currently being tested for proper gene expression.
The development of mulberry plant with transgenic gene HVA-1
Drought and salinity resistant
Transformation of mulberry with hva1 gene from barley for drought and salinity (Lal et al. 2008; Checker et al. 2011).
Tobacco osmotin gene that generates abiotic as well as biotic stress tolerant mulberry (Das et al. 2010).
50

51. Discovery of G protein–coupled receptors
G protein–coupled receptors (GPCRs) are largest integral membrane proteins
that communicate signals across the cell membrane through their interaction
with heterotrimeric G proteins and regulate many of physiological processes
of Bombyx mori such as neurotransmission, growth, development etc.
The GPCRs of the silkworm are identified using the computational methods.
Rhodopsin-like receptors (Class A), secretin receptors (Class B),
metabotropic glutamate/pheromone receptors (Class C), fungal mating
pheromone receptors (Class D), cyclic AMP receptors (Class E), and
frizzled/smoothened GPCRs (Class F).
51

52. Bioinformatic Analysis, and Expression of Bombyx mori Lebocin 5 Gene Related to
Beauveria bassiana Infection
A full length c DNA of Lebocin 5 (BmLeb5) was first cloned from silkworm Bombyx mori by rapid
amplification of c DNA ends. The (BmLeb5 gene is 808bp in length.
Bioinformatics analysis results showed that BmLeb5 owns an O-glycosylation site and four RXXR motifs as
other Lebocins.
Sequence similarity and phylogenic analysis results indicated that lebocins form a multiple gene family in
silkworm as cecropins.
Quantitative real-time PCR analysis revealed that BmLeb5 was highest expressed in the fat body in the
silkworm larvae infected by Beauveria bassiana, the expression level of BmLeb5 was upregulated in the fat
body and hemolymph which are the most important immune tissues in silkworm
52(Lu et al., 2017)

53. Transgenic silkworms
With the introduction of transgenic silkworm hybrids, the quality parameters with reference
to silk grade get improved as compared to the present commercial hybrids.
Development of transgenic silkworms resistant to BmNPV virus
Silkworms are genetically modified to produce human collagen proteins and spider silk
Scientists in Japan have genetically engineered silkworms to create red, green or orange silks
that glow under fluorescent lights.
53

54. Antibody production using TG silkworms
Precocious metamorphosis in transgenic silkworms overexpressing
juvenile hormone esterase.
Resistance of transgenic silkworm to BmNPV could be improved
by silencing ie-1 and lef-1 genes.
Overexpression of host plant urease in transgenic silkworms
Generation of transgenic silkworms for production of erythropoietin
in Bombyx mori.
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56. 56

58. (Singh et al., 2016)58
http://www.ab.a.u-tokyo.ac.jp/silkbase/
http://www.ag.auburn.edu/enpl/hyche/saturniidae/
http://amigo.geneontology.org/cgi-bin/amigo/
blast.cgi www.arthropodgenomes.org/wiki/i5K
http://www.bioinformaticsonline.org
http://www.butterflybase.org
http://ca.expasy.org/sprot/
http://www.cdfd.org.in/silksatdb
http://www.cdfd.org.in/wildsilkbase/team.php
http://www.ebi.ac.uk/ http://www.fruitfly.org
https://www.genevestigator. ethz.ch.
http://insects.eugenes.org/DroSpeGe/
http://www.issas.ac.cn http://www.jassilks.com
http://kaiko2ddb.dna.affrc.go.jp
http://morus.swu.edu.cn/morusdb
http://www.naas.go.kr/ http://www.ncbi.nlm.nih.gov/
http://www.nias.affrc.go.jp http://pir.georgetown.edu/
www.pubmedcentral.nih.gov/
http://resourcedb.nbrp.jp/resource/list.jsp
http://sgp.dna.affrc.go.jp/index.html
http://www.shigen.nig.ac.jp/silkwormbase/index.jsp
http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/index.cgi
http://www.silkgermplasm.com

59. SILKPROT: An Annotated Protein database for Silkworm
SilkProt is a comprehensive, fully annotated, organism specific database for
silkworm proteins.
The database structure will support users to perform a BLAST search with
highly specified and updated latest version of NCBI-BLAST server.
In future this database will be extended for structure visualization and
pathway information of silkworm proteins.
Search page of Silkprot database 59

60. SilkTF-Silkworm Transcription Factor Database
Main page of SilkTF
Transcription factors are the key regulatory proteins that enhance or
repress the transcriptional rates
Regulation of gene expression.
Identification and classification of TFs provide important resources
for researchers especially in the comparative genomics and
transcriptional regulation.
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61. Mulberry Genome Database
Phylogenetic relationship in terms of dendrogram and marker
segregation pattern has been compiled and stored using relational
database with Visual Basic Platform. The database is also made
available in the form of CD.
Search page of morphology of Mulgenomedb
61

62. Soilinfo
This database provides information about the different types of
soils, physical information, physico-chemical properties,
primary and secondary micronutrients etc.
Main page of Soilinfo database
62

63. SilkPPI- Silkworm protein-protein interaction database
The Silkworm, Bombyx mori protein-protein
interaction network were predicted using the
well recognized Interlog method.
Main page of SilkPPI63

64. Database of DNA sequences for important plant genes in mulberry
A database has been developed for storing and
retrieving DNA sequences of important plant genes
responsible for yield, quality, diseases and pest
resistance and also some of the mulberry specific
genes obtained from the public domain.
Search page of important plant genes
64

65. Construction of growth indices in popular breeds/hybrids of silkworm
Bombyx mori L. in relation to nutritional conditions
A software for estimating the Growth Index in silkworm
Bombyx mori has been developed to compare the growth
rate of different silkworm breeds and hybrids under
varying conditions of nutrition.
Main page of Growth index software65

66. BioinfoLib
Under this Bioinformatics Library information system, one can access specialized
bioinformatics centers as well as books, scientific journals, manuals, newsletters
and the information on latest research & development.
Main Page of Bioinfolib
66

67. SilkDis - A Comprehensive Silkworm Disease and Pest Database
Organism specific database featuring the information on the
diseases and pests of the host plant mulberry and the silkworm.
The Database provides detailed information on the diseases and
pests, place, mode of infection, biotic and abiotic factors.
Main Page of SilkDis database
67

68. MulDis: A Comprehensive Mulberry Disease and Pest Database
MulDis an organism specific database featuring
the information on the diseases and pests of the
host plant mulberry and the silkworm.
Main Page of MulDis database68

69. Conclusions
Bioinformatics joins mathematics, statistics, and computer science
and information technology to solve complex biological problems.
The tools of bioinformatics are helpful in every field of life.
In agriculture the genome sequencing of the plants and animals
provides number of benefits.
Seri bioinformatics has energized research and fostered a surge of
new ideas for mulberry and silkworm improvement.
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71. Bioinformaticians are not anti social, they are just genome friendly.