The National Center for Biotechnology Information (NCBI) was established in 1988 as part of the National Library of Medicine. NCBI houses numerous biomedical databases including those related to genes, proteins, molecular structures, gene expression, and biomedical literature. Users can utilize various tools on the NCBI site to search databases, perform sequence alignments using BLAST, and submit new sequences. Some key databases include GenBank (nucleotide sequences), PubMed (biomedical literature), and RefSeq (non-redundant reference sequences).
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.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
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.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
Protein structure classification/domain prediction: SCOP and CATH (Bioinforma...SELF-EXPLANATORY
This pdf is about the protein structure classification/domain prediction: SCOP and CATH (Bioinformatics).
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
Genomic databases are referred to as online repositories of genomic variants, described for a single (locus-specific) or more (general) genes or specifically for a population or ethnic group (national/ethnic).
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
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
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
Protein structure classification/domain prediction: SCOP and CATH (Bioinforma...SELF-EXPLANATORY
This pdf is about the protein structure classification/domain prediction: SCOP and CATH (Bioinformatics).
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
Genomic databases are referred to as online repositories of genomic variants, described for a single (locus-specific) or more (general) genes or specifically for a population or ethnic group (national/ethnic).
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
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
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
JEVBase: An Interactive Resource for Protein Annotationof JE VirusCSCJournals
Databases containing proteome ic information have become indispensable for virology related studies. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has compiled and maintained a functional and molecular annotation database (http://www.jevbase.biomedinformri.org) commonly referred to as JEVBase. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Japanese encephalitis virus (JEV). Identification of different protein functions and molecular analysis facilitates a mechanistic understanding of (JEV) infection and opens novel means for drug development. JEVBase database aims to be a resource for scientists working on JE virus
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(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 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.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Lateral Ventricles.pdf very easy good diagrams comprehensive
Ncbi
1. NCBI
National Centre For Biotechnology
Information
Site: www.ncbi.nlm.nih.gov
By Richa Sharma
M.Sc. Biomedical Sciences
Dr. BR Ambedkar Center for Biomedical
aresearch (ACBR)
2. INTRODUCTION
NCBI was established in the year 1988, as a part of the
National Library of Medicine at the National Institutes of
Health, Maryland, USA
4. DIFFERENCES BETWEEN
DATABASE AND TOOL
DATABASE
It is a collection of data
that is structured,
searchable, updated
periodically and cross-
referenced.
Different databases are:
Genome Database
Sequence Database
Protein Database
Literature Database
Disease Database
TOOL
A program that is used to
extract or retrieve the
desired information from
the database.
Different types of tools are:
Database Retrieval Tool i.e.
Entrez
BLAST
ORF Finder
ePCR
Spidey
7. DATABASE RETRIEVAL TOOL-
ENTREZ
Entrez is an integrated database search and retrieval
system that extracts information from DNA and protein
sequence data, population sets, whole genome,
macromolecular structures, and the biomedical literature
via PubMed.
Entrez provides extensive links within and between
database records.
http://www.ncbi.nlm.nih.gov/gquery/
14. BLAST-BASIC LOCAL ALIGNMENT
SEARCH TOOL
The BLAST programs perform sequence-similarity searches
against a variety of sequence databases, returning a set of
gapped alignments with links to full database records, to
UniGene, Gene, the MMDB, or GEO.
The BLAST tools available at NCBI are classified into
different categories.
Two important ones are:
Standard BLAST
MegaBLAST
15. STANDARD BLAST
Standard BLAST includes:
blastn : Comparing the nucleotide sequence query
against a nucleotide sequence database.
blastp : Comparing the amino acid query against a
protein sequence database.
blastx : Comparing the nucleotide query sequence
translated in all reading frames against a protein
database.
16. • tblastn : Comparing the protein query
sequence against a nucleotide database
translated in all reading frames.
tblastx : Comparing the six –reading
frame translations of the nucleotide
query against six frame translations of
the nucleotide sequence database.
17. MegaBLAST
MegaBLAST is a program optimized for aligning long
sequences.
It can only work with DNA sequences, hence the only
program it supports is “blastn”.
It is faster than blastn but less sensitive,
18. SEQUENCE SUBMISSION TO NCBI
The databases are constantly updated through newer
submissions of sequences, and this is done using the
following sequence submission tools :
1. BankIt
2. Sequin
19. BankIt
BankIT is a web based GenBank sequence submission tool.
It is a tool of choice for simple submissions, especially
when only one or small number of records are to be
submitted. It can also be used by submitters to update
their existing GenBank records. Sequence analysis tools are
not required for submission through this process.
20. SEQUIN
Sequin is a stand-alone software tool developed by NCBI
which aids in submission and updating entries to the
sequence databases. It helps in handling multiple
sequence submissions, provides increased capacity for
complex submissions containing long sequences, multiple
annotations, segmented sets of DNA or phylogenetic and
population studies.
It also provides graphical viewing and editing options.
26. SPECIALISED TOOLS
Some of the specialized tools for the sequence analysis are
:
1. ORF Finder
2. e-PCR
3. Spidey
27. Open Reading Frame (ORF)
Finder
ORF Finder is an essential graphical analysis tool, which
finds all open reading frames of a selectable minimum size
in a user’s sequence or in a sequence already in the
database.
It uses the standard or alternative genetic codes to identify
all open reading frames.
This is helpful in preparing complete and accurate
sequence submissions. It is also packaged with the Sequin
sequence submission software.
28. e-PCR (Electronic Polymerase
Chain Reaction)
e-PCR is a computational procedure that is used to identify
sequence-tagged sites (STSs) within DNA sequeces. While
looking for potential STSs in DNA sequences e-PCR searches
for sub-sequences that closely match the PCR primers and
have the correct order, orientation, and spacing that could
represent the PCR primers used to generate known
STSs.The new version of e-PCr provides a search mode
using a query sequence against a sequence database.
29. SPIDEY
This is an m-RNA to genomic alignment program ,which
uses the local alignment tools like BLAST to find its
alignment. Spidey takes as an input a single genomic
sequence and a set of mRNA-FASTA sequences. At first,
Spidey defines windows on the genomic sequence and then
perform the mRNA-to-genomic alignment separately within
each window to avoid including exons from paralogs and
pseudogenes. It has no maximum intron size and does not
favour shorter or longer introns.
30. Databases
Structured collection of information.
Consists of basic units called record or enteries.
The prefect database-
Comprehensive but easy to search
Cross referenced
Minimum redundancy
31. NCBI Databases
Nucleotide database
Literature database
Protein database
Gene expression database
Structural database
Chemical database
Other databases
32.
33. Kinds of databases
Primary database
Original submissions by
experimentalists.
Database staff organise
but don’t add additional
information.
Example - Genbank
Derivative databases
Derived from primary
data
Content controlled by
third party.
Examples – Refseq,
SWISS-PROT, unigene
34. Nucleotide database
GENBANK
NCBI’s primary sequence data
It is a comprehensive public database of nucleotide
sequences.
Genbank along with EMBL and DDBJ comprises the INSD.
It is a collaborative approach for exchanging data daily
to ensure a uniform and comprehensive collection of
sequence information.
35.
36. Accession numbers are labels for
sequences
DNA sequences and other molecular data are tagged with
accession numbers that are used to identify a sequence or
other record relevant to molecular data.
It is string of letters and/or numbers that corresponds to a
molecular sequence.
It is shared among the 3 collaborating databases and
remains constant over the lifetime of record.
The DNA sequence within a Genbank record is also assigned
a unique NCBI identifier called a ‘gi’ that apperas on the
version line of flat file records following the accession
number.
43. NCBI’s Derivative Sequence
Database
RefSeq
It is a collection of non redundant set of nucleotide and
protein sequences.
It is derived from the primary submissions available in the
GenBank.
RefSeq records can be distinguished from GenBank records
by the format of the accession series
RefSeq accession numbers are formatted as two alphabetic
characters followed by an underscore ‘-’
The GenBank accession never include an underscore.
44. Literature database
PMC – PubMed Central
It is a digital archive of peer-reviewed journals in the
life sciences providing access to full-text articles.
All PMC free articles are identified in PubMed search
results and PMC itself can be searched using Entrez.
49. Protein database
Entrez protein is the protein sequence database of NCBI.
The protein sequences in this database come from several
different sources such as Swiss-Prot,PDB.
There are GenPept translations for each of the coding
sequences within the GenBank nucleotide database.
The Entrez protein database is cross linked to the Entrez
taxonomy database.
It is also linled to CDD.
After clicking on the individual search results of Entrez
protein,the protein sequence is displayed in a particular
format which is known as GenPept.
50. Expression database
GEO-Gene Expression Omnibus
Distribution and regulation of the transcriptional
products of normal and abnormal cell types.
SAGE map- serial analysis of gene expression map.
51. Structural database
MMDB-Molecular modelling database.
3D macromolecular structures.
XRD and NMR are being used for the experimental structure
determination.
These provide a wealth of information regarding the biological
function,mechanism linked to the function,the evolutionary history of the
function and relationship between the macromolecules.
52. Chemical database
PubChem is a database of chemical molecules
maintained by NCBI.
It focuses on the chemical,structural and biological
properties of small molecules
Molecular mass below 2000u.
53. Other databases
OMIM-Online Mendelian Inheritance in Man.
It is a comprehensive,authoritative and timely
knowledge base of human genes and genetic disorders.
OMIA-Online Mendelian Inheritance in Animals.
It is a database of genes,inhertited disorders and traits
in animal species other than human and mouse.