This document discusses biological databases and provides information about GenBank. It defines biological databases as structured collections of biological information consisting of records with predefined fields. It then describes GenBank as the primary database for nucleotide sequences, containing over 100,000 organism sequences submitted from laboratories worldwide. GenBank is one of three major sequence databases that share data daily and is accessible through NCBI's retrieval system Entrez.
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
Course: Bioinformatics for Biomedical Research (2014).
Session: 1.2- Storing and Accessing Information. Databases and Queries.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology
Exploring DNA/RNA-Seq Analysis Results with Golden Helix GenomeBrowse and SVSGolden Helix Inc
GenomeBrowse, a free visualization tool for all types of sequence data, was introduced in 2012 to broad acclaim. Researchers using GenomeBrowse discovered a product far beyond the status quo with seamless navigation of sequence alignments and other genomic data using a fluid, fast, and intuitive interface that just "made sense." Recent updates to GenomeBrowse, including support for VCF files and BED files and the ability to export tables of data extracted from viewable annotation tracks, further improved the product and created new synergy with Golden Helix SNP & Variation Suite (SVS).
This webcast will demonstrate the ability of GenomeBrowse to stream sequence alignment data from the Amazon Cloud, seamlessly transitioning between whole genome views and base-pair resolution in the context of both public and custom annotation tracks. We will show how GenomeBrowse can be used in conjunction with SVS to highlight false variant calls, confirm the inheritance pattern of putative functional variants, and aid in the interpretation of a variant's impact. Examples of RNA-seq expression analysis, somatic variation in cancer, and family-based DNA-seq analysis will be included.
"A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information."
Genomic Big Data Management, Integration and Mining - Emanuel WeitschekData Driven Innovation
Thanks to Next Generation Sequencing (NGS), a technology that is lowering the cost and time of reading DNA, we are faced with huge amounts of biomedical data. These data are continuously collected by research laboratories, and often organized through world-wide consortia, which are releasing many public data bases. One of the main aims of bioinformatics is to solve fundamental issues in biomedicine research (e.g., how cancer occurs) starting from big genomic data and their analysis. In this talk I will give an overview of big genomic data management, integration, and mining.
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
CLASS 11 CBSE B.St Project AIDS TO TRADE - INSURANCE
Biological databases
1. 10/11/2017
1
Biological Databases
Dr. Ayaz Ahmad
2
Biological databases
1. Biological information and databases
– Overview and definition, types of biological databases
2. Popular databases, records, data format
– Genbank, SwissProt, OMIM, PDB, KEGG, BIND, Pfam, PROSITE, PubMed
3. Accessing biological databases, retrieval systems
– Entrez, SRS
4. Searching biological databases
– Data quality, coverage, redundancy, errors
Textbook:
--T.K.Atwood and D.J. Parry Smith, Introduction to Bioinformatics.
Biological databases: chapters 3 and 4
2. 10/11/2017
2
3
Biological Information
Nucleic acids:
• DNA sequence, genes, gene products (proteins), mutation,
gene coding, distribution patterns, motifs
• Genomics: genome, gene structure and expression, genetic
map, genetic disorder
• RNA sequence, secondary structure, 3D structure,
interactions
Proteins:
• Protein sequence, corresponding gene, secondary structure,
3D structure, function, motifs, homology, interactions
• Proteomics: expression profile, proteins in disease processes
etc.
• Ligands and drugs (inhibitors, activators, substrates,
metabolites)
4
Biological Information
Pathways:
• Molecular networks, biological chain events,
regulation, feedback, kinetic data
Function:
• Binding sites, interactions, molecular action
(binding, chemical reaction, etc.)
• Biological effect (signaling, transport, feedback,
regulation, modification, etc.)
• Functional relationship, protein families, motifs, and
homologs
3. 10/11/2017
3
WHAT IS A DATABASE?
• Structured collection of information.
• Consists of basic units called records or entries.
• Each record consists of fields, which hold pre-defined
data related to the record.
• For example, a protein database would have protein
entries as records and protein properties as fields (e.g.,
name of protein, length, amino-acid sequence)
THE ‘PERFECT’ DATABASE
• Comprehensive, but easy to search.
• Annotated, but not “too annotated”.
• A simple, easy to understand structure.
• Cross-referenced.
• Minimum redundancy.
• Easy retrieval of data.
4. 10/11/2017
4
7
Biological databases
Purpose
1. To disseminate biological data and information
2. To provide biological data in computer-readable form
3. To allow analysis of biological data
TYPES OF MOLECULAR DATABASES
• Primary Databases
– Original submissions by experimentalists
– Content controlled by the submitter
• Examples: GenBank, Trace, SRA, SNP, GEO
• Derived Databases
– Derived from primary data
– Content controlled by third party (e.g. NCBI)
• Examples: NCBI Protein, Refseq, TPA, RefSNP, GEO
datasets, UniGene, Homologene, Structure,
Conserved Domain
5. 10/11/2017
5
PRIMARY VS. DERIVED SEQUENCE
DATABASES
GenBank
Sequencing
Centers
TATAGCCG TATAGCCGTATAGCCG TATAGCCG
Labs
Algorithms
UniGene
Curators
RefSeq
Genome
Assembly
TATAGCCG
AGCTCCGATA
CCGATGACAA
Updated
continually
by NCBI
Updated ONLY
by submitters
Bibliographic Databases
Integrated Databases
Structural Databases
Sequence Databases
Clinical Databases
Types of Biological Databases
6. 10/11/2017
6
“Ten Important Bioinformatics Databases”
GenBank www.ncbi.nlm.nih.gov nucleotide sequences
Ensembl www.ensembl.org human/mouse genome
(and others)
PubMed www.ncbi.nlm.nih.gov literature references
NR www.ncbi.nlm.nih.gov protein sequences
SWISS-PROT www.expasy.ch protein sequences
InterPro www.ebi.ac.uk protein domains
OMIM www.ncbi.nlm.nih.gov genetic diseases
Enzymes www.chem.qmul.ac.uk enzymes
PDB www.rcsb.org/pdb/ protein structures
KEGG www.genome.ad.jp metabolic pathways
Source: Bioinformatics for Dummies
12
GenBank
http://www.ncbi.nih.gov/Genbank/
7. 10/11/2017
7
13
GenBank database
(http://www.ncbi.nih.gov/Genbank/)
– Contains publicly available DNA sequences from more than
100,000 organisms.
– Also contains derived protein sequences, and annotations
describing biological, structural, and other relevant features.
– Accessible through Entrez, NCBI’s integrated retrieval system
– Sequence similarity search tools: BLAST
GenBank
• Annotated collection of all publicly
available nucleotide sequences and their
protein translations.
• Receives sequences produced in
laboratories throughout the world from
more than 100,000 distinct organisms.
• Grows exponentially, doubling every 10
months
8. 10/11/2017
8
GENBANK - PRIMARY SEQUENCE DB
http://www.ncbi.nlm.nih.gov/genbank/
• Nucleotide only sequence database
• Archival in nature
– Historical
– Reflective of submitter point of view
– Redundant
• Data
– Direct submissions
– Batch submissions
– FTP accounts (genome data)
GenBank
•Data shared nightly among three
collaborating databases
•GenBank at NCBI
•DNA Database of Japan (DDBJ)
•EMBL at EBI
9. 10/11/2017
9
The International Sequence Database Collaboration
Source NCBI
GeneBank Release 220
June 2017
• full release every two months
• incremental and cumulative updates daily
• available only through internet
ftp://ftp.ncbi.nih.gov/genbank/
10. 10/11/2017
10
GenBank Record
➢ Header
information that apply to
the whole record
➢ Features
annotations on the record
➢ Sequence
GeneBank Record
modification
date
Header
Locus Name
Sequence Length
Molecule Type
GenBank Division
Modification DateAccession Number
Version Number
12. 10/11/2017
12
Direct Submission
• A typical GenBank submission consists of
a single, contiguous stretch of DNA or
RNA sequence (contigs) with annotations
(metadata).
• If part of a nucleotide sequence encodes a
protein, a conceptual translation, called a
CDS (coding sequence) is annotated.
High-Throughput Genomic
Sequence (HTGS)
• HTGS entries are submitted in bulk by
genome centers, processed by an
automated system, and then released to
GenBank.
• Currently, more than 30 genome centers
are submitting data for a number of
organisms, including human, mouse, rat,
rice, and Plasmodium falciparum.
13. 10/11/2017
13
Whole Genome Shotgun
Sequences (WGS)
• Shotgun sequence reads are assembled into contigs,
submitted, and updated as the sequencing project
progresses and new assemblies are computed.
Submission Tools
• BankIt: Web-based form for submission of
a small number of sequences with minimal
annotation to GenBank.
• Sequin: More appropriate for complicated
submissions containing a significant
amount of annotation or many sequences.
14. 10/11/2017
14
Sequence Data Flow and
Processing
• Within 48 hours of direct submission with BankIt or Sequin,
the database staff reviews the submission to determine
whether it meets the minimal criteria and then assigns an
Accession number.
– All sequences must be > 50 bp in length and be sequenced by,
or on behalf of, the group submitting the sequence.
– GenBank will not accept sequences constructed in silico
– GenBank will not accept noncontiguous sequences containing
internal, unsequenced spacers.
– GenBank will not accept sequences for which there is no
physical counterpart, such as those derived from a mix of
genomic DNA and mRNA.
– Submissions are checked to determine whether they are new or
updates.
Sequence Data Flow and
Processing
• Indexing:
– Biological validity: Translation, organism lineage, BLAST
searches
– Vector contamination: Is there any vector DNA present in the
sequence?
– Publication status: If published, citation is included in annotation
and linked to Entrez
– Formatting and spelling
• Sequences are sent to submitter for final review before
release into the public database.
• Sequences must become publicly available once the
accession number or the sequence has been published.
• GenBank annotation staff process about 1900
submissions/month, or about 20,000 sequences.
15. 10/11/2017
15
Essential Bioinformatics and
Biocomputing (LSM2104), NUS 29
DNA databases
• An Example from GenBank– flat file
– Human Alpha-Lactalbumin gene
This protein is a complex of 2 proteins A and B. In the absence of the
B protein, the enzyme catalyzes the transfer of
galactose from UDP-galactose to Nacetylglucosamine (cf. EC 2.4.1.90).
Essential Bioinformatics and
Biocomputing (LSM2104), NUS 30
A GenBank entry – HEADER
16. 10/11/2017
16
31
GenBank Entry – Links provided in the Header
• MapViewer – find the gene position in chromosome
• Related Sequences – other entries related to this gene (or sequence)
• OMIM– link to catalog of human genes and genetic disorders
• Protein – retrieve protein record from GenPept
• Medline and PubMed –literature abstracts related to this gene
• Taxonomy – Classification of organisms
• UniGene – Unified gene data
• UniSTS – Unified sequence tagged sites, marker and mapping data
• LinkOut – links to publishers, aggregators libraries, biological databases,
sequence centers, and other Web resources
• REFSEQ – reference sequence standards
Note: These links are representative. Other links may also be found in GenBank
entries.
Essential Bioinformatics and
Biocomputing (LSM2104), NUS 32
GenBank entry - FEATURES
