INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVES OF BIOINFORMATICS
TOOLS OF BIOINFORMATICS
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
INTRODUCTION OF BIOINFORMATICS
HISTORY
WHAT IS DATABASE
NEED FOR DATABASE
TYPES OF DATABASE
PRIMARY DATABASE
NUCLEIC ACID SEQUENCE DATABASE
GENE BANK
INTRODUCTION
GENE BANK SUBMISSION TOOL
GENE BANK SUBMISSION TYPE
HOW TO RETRIEVE DATA FROM GENEBANK
APPLICATION
CONCLUSION
REFERENCE
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
INTRODUCTION OF BIOINFORMATICS
HISTORY
WHAT IS DATABASE
NEED FOR DATABASE
TYPES OF DATABASE
PRIMARY DATABASE
NUCLEIC ACID SEQUENCE DATABASE
GENE BANK
INTRODUCTION
GENE BANK SUBMISSION TOOL
GENE BANK SUBMISSION TYPE
HOW TO RETRIEVE DATA FROM GENEBANK
APPLICATION
CONCLUSION
REFERENCE
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
Bioinformatics Introduction and Use of BLAST ToolJesminBinti
Hi, I am Jesmin, studying MCSE. I think this file will help you if you want to know the basic information about Bioinformatics and the use of BLAST tool. The BLAST tool is the tool that matches the sequences of DNA,RNA and proteins.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
Abstract-GasCan is a specialized and unique database of gastric cancer protein encoding genes expressed in human and mouse. The features that make GasCan unique are availability of gene information, availability of primers for each gene, with their features and conditions given that are useful in PCR amplification, especially in cloning experiments and to make it more unique built in programmed sequence analysis facility is provided that analyze gene sequences in database itself, resulting sequence analysis information can be valuable for researchers in different experiments. Furthermore, DNA sequence analysis tool is provided that can be access freely. GasCan will expand in future to other species, genes and cover more useful information of other species. Flexible database design, expandability and easy access of information to all of the users are the main features of the database. The Database is publicly available at http://www.gastric-cancer.site40.net.
GASCAN: A Novel Database for Gastric Cancer Genes and Primersijdmtaiir
GasCan is a specialized and unique database of
gastric cancer protein encoding genes expressed in human and
mouse. The features that make GasCan unique are availability
of gene information, availability of primers for each gene, with
their features and conditions given that are useful in PCR
amplification, especially in cloning experiments and to make it
more unique built in programmed sequence analysis facility is
provided that analyze gene sequences in database itself,
resulting sequence analysis information can be valuable for
researchers in different experiments. Furthermore, DNA
sequence analysis tool is provided that can be access freely.
GasCan will expand in future to other species, genes and cover
more useful information of other species. Flexible database
design, expandability and easy access of information to all of
the users are the main features of the database. The Database is
publicly available at http://www.gastric-cancer.site40.net.
With advances in technology, enormous amounts of data have become available for bioscience researchers. While this high volume of information holds tremendous promise for expanding the science knowledge base, it must be organized for meaningful study. Bioinformatics is a discipline that devises methods for storing, distributing, and analyzing biological data used by diverse areas of research. Bioinformatics professionals develop software and tools that assist researchers in the analysis of data related to molecular biology and genome studies.
Bioinformatics in biotechnology by kk sahu KAUSHAL SAHU
Introduction
Bioinformatics – definition
History
Required skills
Core areas of bioinformatics
Components of bioinformatics
Nomenclature system in bioinformatics
Biological databases
Types of database
Bioinformatics tools
Applications of bioinformatics
Conclusion
References
Introduction
History
Tumor suppressor gene- pRB
- RB gene
- Role of RB in regulation of cell cycle
- Tumor associated with RB gene mutation
Tumor suppressor gene- p53
- What is p53 gene?
- Function of p53 gene
- How it regulates cell cycle
- What happen if p53 gene inactivated
- Cancer associated with p53 mutation
- Conclusion
- References
Introduction
Definition
History
Two hit hypothesis
Functions
Mutation in tumor suppressor genes
What is mutation
Inherited mutation of TSGs
Acquired mutation of TSGs
What is Oncogenes?
TSGs and Oncogenes : Brakes and accelerators
Stop and go signal
Examples of TSGs:
RB-The retinoblastoma gene
P53 protein
TSGs &cell suicide
Conclusion
References
Introduction
Protein synthesis
Synthesis of secretory proteins on membrane-bound ribosomes
Processing of newly synthesized proteins in the ER
Synthesis of integral membrane protein on membrane bound ribosomes
Maintenance of membrane asymmetry
Conclusion
Reference
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
Introduction
Definition
History
central dogma
Major components
mRNA,tRNA,rRNA
Energy source
Amino acids
Protien factor
Enzymes
Inorganic ions
Step involves in translation:
Aminoacylation of tRNA
Initiation
Elongation
termination
Importance of translation
Conclusion
Reference
Introduction
Protein modifications
Folding
Chaperon mediated
Enzymatic
Cleavage
Addition of functional groups
Chemical groups
Hydrophobic groups
Proteolysis
Conclusion
Reference
INTRODUCTION
HISTORY
WHAT IS TRANSCRIPTION
PROKARYOTIC TRANSCRIPTION
STEPS OF TRANSCRIPTION
HOW TRANSCRIPTION OCCURS
PROCESS OF TRANSCRIPTION
Initiation
Elongation
Termination
CONCLUSION
REFRENCES
Enzyme Kinetics and thermodynamic analysisKAUSHAL SAHU
Introduction
Kinetics and thermodynamicSG
Thermodynamic in enzymatic reactions
balanced equations in chemical reactions
changes in free energy determine the direction & equilibrium state of chemical reactions
the rates of reactions
Factors effecting enzymatic activity
(i) Enzyme concentration.
(ii) Substrate concentration.
(iii)Temperature
(iv) pH.
(v) Activators.
(vi)Inhibitors
Michaelis-menten equation
CONCLUSIONS
REFERENECES
Recepter mediated endocytosis by kk ashuKAUSHAL SAHU
INTRODUCTION
DEFINITION OF RECEPTOR MEDIATED ENDOCYTOSIS
WHAT TYPE OF LIGANDS ENTER BY RME?
FORMATION OF CLATHRIN-COATED VESICLES
TRISKELIONS
ROLE OF DYNAMIN IN THE FORMATION OF CLATHRIN-COATED VESICLES
ROLE OF PHOSPHOLIPIDS IN THE FORMATION OF COATED VESICLES
ENDOCYTIC PATHWAY
LDLs AND CHOLESTROL METABOLISM
CONCLUSION
REFERENCES
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Prokaryotic translation machinery by kk KAUSHAL SAHU
Introduction
Definition
Factors required for Translation
Formation of aminoacyl t-RNA
1)Activation of amino acid
2) Transfer of amino acid to t-RNA
Translation involves following steps:-
1)Initiation
2)Elongation
3)Termination
Conclusion
Reference
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
2. INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVES OF BIOINFORMATICS
TOOLS OF BIOINFORMATICS
o BIOLOGICAL DATABASES
o HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE
ALIGNMENT)
o PROTEIN FUNCTION ANALYSIS TOOLS
o STRUCTURAL ANALYSIS TOOLS
o SEQUENCE MANIPULATION TOOLS
o SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
11-May-20
2
3. Bioinformatics is a newly emerged scientific discipline
for the computational analysis and storage of biological
data. The word bioinformatics has been derived from
two words.
Bio means biology
Informatics (a French word) meaning ‘data processing’.
Bioinformatics is the field in which biology, computer
science and information technology merge into single
discipline for managing and analyzing biological data
using advanced computing techniques.
11-May-20
3
4. Keeping in view all the facts, bioinformatics can be
defined as the storage, analysis, and searching/retrieval
of data(e.g. nucleic acid sequences for the genes and
RNAs, amino acid sequence and structural information of
protein).
Fredj Tekaia at the Institute Pasteur, Paris (France)
defined bioinformatics more precisely as the
mathematical, statistical and computing methods that
aim to solve biological problems using DNA and amino
acid sequences, and related information.
11-May-20
4
5. YEAR’S SCIENTIST HISTORICAL EVENTS
1958 Jack Kilby The first integrated circuit (IC) was constructed.
1971 Ray Tholinson The e-mail program was invented.
1974 Vint Cerf & Robert
Khan
The concept of connecting network of computer into an “internet”
and develop the Transmission Control Protocol (TCP) was
developed.
1981 PC IBM introduces its Personal Computer to the market.
1984 The Macintosh was announced by Apple Computer.
1986 SWISS-PROT The SWISS-PROT database was created by the Department of
Medical Biotechnology of the University of Geneva and the
European Molecular Biology Laboratory (EMBL).
1987 HGI (Human
Genome Initiative)
NIH NIGMS begun funding of genome projects.
1990 BLAST The BLAST program is implemented.
1991 Birth of term
“Bioinformatics”
First time the term Bioinformatics appeared in the scientific
literature.
11-May-20
5
6. At its simplest and basic level, bioinformatics organizes data in a way
that allows researchers to access existing information and to submit
new entries, as produced (e.g.) the protein data Bank for 3D
macromolecular structures.
The second key objective is to develop tools and resources that aid in
the analysis of data. For example, having sequenced a particular
protein, it is of interest to compare it with previously characterized
sequences.
The third objective is to use these tools to analysis the data and
interpret the results in a biologically meaningful manner. Traditionally,
biological studies examined individual systems in detail, and frequently
compared them with a few that are related.
11-May-20
6
7. These are software programs that are designed for
extracting the meaningful information from the mass of
molecular biology/biological databases and to carry out
sequence and structural analysis.
After the formation of the databases, tools become
available to search sequences databases.
The bioinformatics tools can be categorized in to the
following categories:
a) Biological databases
b) Homology and similarity tools (Sequence alignment tool)
c) Protein function analysis tools
d) Structural analysis tools
e) Sequence manipulation tools
f) Sequence analysis tools
11-May-20
7
8. This biological database usually contain genomic, proteomic and
metabolic data. The data include nucleotide sequences of genes or
amino acid sequences.
Some of the major biological database are:
a) Major Nucleotide Sequences Database.
b) Major Mutation Databases.
c) Major Gene Expression Databases.
d) Major Microbial Genomic Databases.
e) Major Organism Specific Genome Database.
f) Major protein Database.
EMBL (European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton,
UK)
NDB (Nucleic Acid structure Database at Rutgers University, USA)
Entrez/Genome (NCBI, USA)
11-May-20
8
9. Homologous sequences are sequences that are
related by divergence from a common ancestor.
Thus the degree of similarity between two
sequences can be measured.
This set of tools can be used to identify
similarities between novel query sequences of
unknown structure and function and database
sequences whose structure and functions have
been elucidated.
11-May-20
9
10. o It is a program for sequence similarity searching
developed at the NCBI.
o It identifies genes and genetic features.
o It executes sequences searches against the entire DNA
database in less than 15 seconds.
o A BLAST search enables a researcher to compare a
query sequence with a database of sequence and
identify database sequence that resemble the query
sequence.
11-May-20
10
11. FASTA is a DNA and protein sequence alignment software
package.
It is used for a fast protein or fast nucleotide comparison.
This program achieves a high level of sensitivity for
similarity searching at high speed.
11-May-20
11
12. These groups of programs allow comparing protein
sequence to the secondary protein databases that contain
information on motifs, signatures and protein domains.
Interproscan
Search protein sequences.
PPSearch
Searches protein motifs.
Radar
Protein repeats detection.
11-May-20
12
13. This set of tools allows comparing structures with the known
structures databases. The determination of a protein’s 2D/3D
structure is crucial in the study of its functions.
RasMol
It is a powerful research tool to display the structure of biological
macromolecules like DNA, proteins and smaller molecules.
PROSPECT(PROtein Structure Prediction and Evaluation
Computer Toolkit)
It is a protein structure prediction system that employs a
computational technique called protein threading to construct a
protein 3-D model.
COPIA(Consensus Pattern Identification and Analysis)
It is a protein structure analysis tool for discovering motifs in a
family of protein sequences. Such motifs can then be used to
determine membership to the family of new proteins sequences,
predict secondary and tertiary structures and functions of proteins.
11-May-20
13
14. These are software programs for analyzing and formatting
DNA and protein sequences.
RepeatMasker
It is a program that screens the DNA for interspersed
repeats.
Webcut
It is an online tool for restriction analysis, silent
mutation analysis, and SNP analysis.
Translate
It is a tool which allows the translation of a nucleotide
sequence to a protein sequence.
11-May-20
14
15. This set of tools allow to carry out further more detailed
analysis of query sequence including evolutionary
analysis, identification of mutation.
Align
This tool is used to compare two sequences.
DNA Scanner
It is a tool that scans DNA for number of different
properties such as biophysical, potential for protein
interaction.
11-May-20
15
16. Some of the applications related to biological
information analysis are:
Bioinformatics is used in primer design.
Bioinformatics is used to attempt to predict the function
of actual gene products.
Molecular modeling/structural biology is a growing field
which can be considered part of bioinformatics.
There are other fields- for example, medical imaging/
image analysis, that might be considered part of
bioinformatics. there is also a whole other discipline of
biologically inspired computation: genetic algorithms, AI,
neural networks etc.
11-May-20
16
17. Bioinformatics is building on the recognition of the
importance of information transmission, accumulation
and processing in biological systems.
Software tools for bioinformatics range from simple
command-line tools, to more complex graphical programs
and standalone web-services available from various
bioinformatics companies or public institutions.
11-May-20
17