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.
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.
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
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.
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
STS stands for sequence tagged site which is short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
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.
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.
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
Aim1: To study the method of genome identification through ENSEMBL browser.
Aim2: To study the method of genome identification through VISTA.
Aim3: To study the method of genome identification through UCSC Genome Browser.
Aim4: To study the method of genome and amino acid sequences through UCSC Genome Browser.
PERFORMANCE EVALUATION OF STRUCTURED AND SEMI-STRUCTURED BIOINFORMATICS TOOLS...ijseajournal
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased interfaces. These methods retrieve bioinformatics information using structured and semi-structured data tools, which are able to retrieve data from remote database servers. This study distinguishes each of these approaches and contrasts these tools. We used Sequence Retrieval System (SRS) and Entrez search tools for structured data, while Perl and BioPerl search programs were used for semi-structured data to retrieve complex queries including a combination of text and numeric information. The study concludes that the use of semi-structured data tools for accessing bioinformatics databases is a viable alternative to the structured tools, though each method is shown to have certain inherent advantages and disadvantages.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
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.
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.
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Yeast two-hybrid is based on the reconstitution of a functional transcription factor (TF) when two proteins or polypeptides of interest interact. Upon interaction between the bait and the prey, the DBD and AD are brought in close proximity and a functional TF is reconstituted upstream of the reporter gene.
Aim1: To study the method of genome identification through ENSEMBL browser.
Aim2: To study the method of genome identification through VISTA.
Aim3: To study the method of genome identification through UCSC Genome Browser.
Aim4: To study the method of genome and amino acid sequences through UCSC Genome Browser.
PERFORMANCE EVALUATION OF STRUCTURED AND SEMI-STRUCTURED BIOINFORMATICS TOOLS...ijseajournal
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased interfaces. These methods retrieve bioinformatics information using structured and semi-structured data tools, which are able to retrieve data from remote database servers. This study distinguishes each of these approaches and contrasts these tools. We used Sequence Retrieval System (SRS) and Entrez search tools for structured data, while Perl and BioPerl search programs were used for semi-structured data to retrieve complex queries including a combination of text and numeric information. The study concludes that the use of semi-structured data tools for accessing bioinformatics databases is a viable alternative to the structured tools, though each method is shown to have certain inherent advantages and disadvantages.
PERFORMANCE EVALUATION OF STRUCTURED AND SEMI-STRUCTURED BIOINFORMATICS TOOLS...ijseajournal
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased interfaces. These methods retrieve bioinformatics information using structured and semi-structured
data tools, which are able to retrieve data from remote database servers. This study distinguishes each of these approaches and contrasts these tools. We used Sequence Retrieval System (SRS) and Entrez search tools for structured data, while Perl and BioPerl search programs were used for semi-structured data to retrieve complex queries including a combination of text and numeric information. The study concludes that the use of semi-structured data tools for accessing bioinformatics databases is a viable alternative to the structured tools, though each method is shown to have certain inherent advantages and disadvantages.
A consistent and efficient graphical User Interface Design and Querying Organ...CSCJournals
We propose a software layer called GUEDOS-DB upon Object-Relational Database Management System ORDMS. In this work we apply it in Molecular Biology, more precisely Organelle complete genome. We aim to offer biologists the possibility to access in a unified way information spread among heterogeneous genome databanks. In this paper, the goal is firstly, to provide a visual schema graph through a number of illustrative examples. The adopted, human-computer interaction technique in this visual designing and querying makes very easy for biologists to formulate database queries compared with linear textual query representation.
Branch: An interactive, web-based tool for building decision tree classifiersBenjamin Good
A crucial task in modern biology is the prediction of complex phenotypes, such as breast cancer prognosis, from genome-wide measurements. Machine learning algorithms can sometimes infer predictive patterns, but there is rarely enough data to train and test them effectively and the patterns that they identify are often expressed in forms (e.g. support vector machines, neural networks, random forests composed of 10s of thousands of trees) that are highly difficult to understand. In addition, it is generally unclear how to include prior knowledge in the course of their construction.
Decision trees provide an intuitive visual form that can capture complex interactions between multiple variables. Effective methods exist for inferring decision trees automatically but it has been shown that these techniques can be improved upon via the manual interventions of experts. Here, we introduce Branch, a new Web-based tool for the interactive construction of decision trees from genomic datasets. Branch offers the ability to: (1) upload and share datasets intended for classification tasks (in progress), (2) construct decision trees by manually selecting features such as genes for a gene expression dataset, (3) collaboratively edit decision trees, (4) create feature functions that aggregate content from multiple independent features into single decision nodes (e.g. pathways) and (5) evaluate decision tree classifiers in terms of precision and recall. The tool is optimized for genomic use cases through the inclusion of gene and pathway-based search functions.
Branch enables expert biologists to easily engage directly with high-throughput datasets without the need for a team of bioinformaticians. The tree building process allows researchers to rapidly test hypotheses about interactions between biological variables and phenotypes in ways that would otherwise require extensive computational sophistication. In so doing, this tool can both inform biological research and help to produce more accurate, more meaningful classifiers.
A prototype of Branch is available at http://biobranch.org/
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.
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.
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in your newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using all available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
The NRNB has been funded as an NIGMS Biomedical Technology Research Resource since 2010. During the previous five-year period, NRNB investigators introduced a series of innovative methods for network biology including network-based biomarkers, network-based stratification of genomes, and automated inference of gene ontologies using network data. Over the next five years, we will seek to catalyze major phase transitions in how biological networks are represented and used, working across three broad themes: (1) From static to differential networks, (2) From descriptive to predictive networks, and (3) From flat to hierarchical networks bridging across scales. All of these efforts leverage and further support our growing stable of network technologies, including the popular Cytoscape network analysis infrastructure.
ANALYSIS OF PROTEIN MICROARRAY DATA USING DATA MININGijbbjournal
Latest progress in biology, medical science, bioinformatics, and biotechnology has become important and
tremendous amounts of biodata that demands in-depth analysis. On the other hand, recent progress in data
mining research has led to the development of numerous efficient and scalable methods for mining
interesting patterns in large databases. This paper bridge the two fields, data mining and bioinformatics
for successful mining of biological data. Microarrays constitute a new platform which allows the discovery
and characterization of proteins.
The problems attract worldwide attention K/a Global Environmental Problems.
The top three environmental problems are: (1) Greenhouse Effect and Global Warming (2) Depletion of Ozone and (3) Acid Rain.
Intracellular Components
We will now begin our discussion of intracellular organelles. As we have mentioned, only eukaryotic cells have intracellular sub-divisions, so our discussion will exclude prokaryotic cells. We will also focus on animal cells, since plant cells have a number of further specialized structures. In this section we will discuss the importance of the cell nucleus, mitochondria, peroxisomes, endoplasmic reticulum, golgi apparatus, and lysosome.
Types of Receptors
Receptors are protein molecules in the target cell or on its surface that bind ligands. There are two types of receptors: internal receptors and cell-surface receptors.
Microbial biomass conversion processes take advantage of the ability of microorganisms to consume and digest biomass and release hydrogen. Depending on the pathway, this research could result in commercial-scale systems in the mid- to long-term timeframe that could be suitable for distributed, semi-central, or central hydrogen production scales, depending on the feedstock used.
The cells derived from root apical and shoot-apical meristems and cambium differentiate and mature to perform specific functions. This act leading to maturation is termed as differentiation. During differentiation, cells undergo few to major structural changes both in their cell walls and protoplasm. The living differentiated cells, that by now have lost the capacity to divide can regain the capacity of division under certain conditions. This phenomenon is termed as dedifferentiation. For example, formation of meristems – interfascicular cambium and cork cambium from fully differentiated parenchyma cells. While doing so, such meristems / tissues are able to divide and produce cells that once again lose the capacity to divide but mature to perform specific functions, i.e., get redifferentiated.
Meat and milk from farmed animals including livestock (cattle, goat and buffalo) and poultry are sources of high quality protein and essential amino acids, minerals, fats and fatty acids, readily available vitamins, small quantities of carbohydrates and other bioactive components.1 The Food and Agriculture Organization (FAO) 2008 estimate shows that meat consumption has grown with increase in population. The average global per capita meat consumption is 42.1 kg/year with 82.9 kg/year in developed and 31.1 kg/year in developing countries in a recommended daily animal-sourced protein per capita of 50 kg per year2. Milk on the other hand is consumed in various forms: liquid, cheese, powder, and cream at a global per capita consumption of 108 kg per person per year which is way below the FAO recommended daily consumption of 200 kg.
Antibodies, also known as immunoglobulins, are secreted by B cells (plasma cells) to neutralize antigens such as bacteria and viruses. The classical representation of an antibody is a Y-shaped molecule composed of four polypeptides-two heavy chains and two light chains. Each tip of the "Y" contains a paratope (a structure analogous to a lock) that is specific for one particular epitope (similarly analogous to a key) on an antigen, allowing these two structures to bind together with precision. The ability of binding to an antigen has led to their ubiquitous use in a variety of life science and medical science. These antibodies can be classified into two primary types (monoclonal and polyclonal) by the means in which they are created from lymphocytes. Each of them has important role in the immune system, diagnostic exams, and treatments.
Hormones, Proteins, etc. present in blood in minute concentration can be assayed by the recent advanced technique of “Enzyme Immuno Assay” without involving any disadvantage. The basic reaction is the interaction between an antibody and an antigen.
Meat and milk from farmed animals including livestock (cattle, goat and buffalo) and poultry are sources of high quality protein and essential amino acids, minerals, fats and fatty acids, readily available vitamins, small quantities of carbohydrates and other bioactive components.1 The Food and Agriculture Organization (FAO) 2008 estimate shows that meat consumption has grown with increase in population. The average global per capita meat consumption is 42.1 kg/year with 82.9 kg/year in developed and 31.1 kg/year in developing countries in a recommended daily animal-sourced protein per capita of 50 kg per year2. Milk on the other hand is consumed in various forms: liquid, cheese, powder, and cream at a global per capita consumption of 108 kg per person per year which is way below the FAO recommended daily consumption of 200 kg.
In shotgun sequencing the genome is broken randomly into short fragments (1 to 2 kbp long) suitable for sequencing. The fragments are ligated into a suitable vector and then partially sequenced. Around 400–500 bp of sequence can be generated from each fragment in a single sequencing run. In some cases, both ends of a fragment are sequenced. Computerized searching for overlaps between individual sequences then assembles the complete sequence.
Sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcript (ESTs).
The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces. Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable.
Vaccine (L. vacca = cow) is a preparation/suspension or extract of dead/attenuated (weakened) germs of a disease which on inoculation (injection) into a healthy person provides temporary/permanent active/passive immunity by inducing antibodies formation.
Thus antibody provoking agents are called vaccines.
Biological treatment is an important and integral part of any wastewater treatment plant that treats wastewater from either municipality or industry having soluble organic impurities or a mix of the two types of wastewater sources.
The four processes are: (1) Preliminary Treatment (2) Primary Treatment (3) Secondary or Biological Treatment and (4) Tertiary or Advanced Treatment
The genetic variations found in the in vitro cultured cells are collectively referred to as somaclonal variations.
The plants derived from such cells are referred to somaclones. Some authors use the terms calliclones and proto-clones to represent cultures obtained from callus and protoplasts respectively.
The growth of plant cells in vitro is an asexual process involving only mitotic division of cells. Thus, culturing of cells is the method to clone a particular genotype. It is therefore expected that plants arising from a given tissue culture should be the exact copies of the parental plant.
The occurrence of phenotypic variants among the regenerated plants (from tissue cultures) has been known for several years. These variations were earlier dismissed as tissue culture artefacts. The term somaclonal variations was first used by Larkin and Scowcraft (1981) for variations arising due to culture of cells, i.e., variability generated by a tissue culture. This term is now universally accepted.
As described elsewhere the explant used in tissue culture may come from any part of the plant organs or cells. These include leaves, roots, protoplasts, microspores and embryos. Somaclonal variations are reported in all types of plant tissue cultures.
In recent years, the term gametoclonal variations is used for the variations observed in the regenerated plants from gametic cells (e.g., anther cultures). For the plants obtained from protoplast cultures, proto-clonal variations is used.
Solid waste management is a polite term for garbage management. As long as humans have been living in settled communities, solid waste, or garbage, has been an issue, and modern societies generate far more solid waste than early humans ever did.
The chemical compounds produced by plants are collectively referred to as phytochemicals. Biotechnologists have special interest in plant tissue culture for the large scale production of commercially important compounds. These include pharmaceuticals, flavours, fragrances, cosmetics, food additives, feed stocks and antimicrobials.
Most of these products are secondary metabolites— chemical compounds that do not participate in metabolism of plants. Thus, secondary metabolites are not directly needed by plants as they do not perform any physiological function (as is the case with primary metabolites such as amino acids, nucleic acids etc.). Although the native plants are capable of producing the secondary metabolites of commercial interest, tissue culture systems are preferred.
The biotic stresses are caused by insects, pathogens (viruses, fungi, bacteria), and wounds. The abiotic stresses are due to herbicides, water deficiency (caused by drought, temperature, and salinity), ozone and intense light.
Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase. Pyrosequencing relies on light detection based on a chain reaction when pyrophosphate is released. Hence, the name pyrosequencing.
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.
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.
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
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!
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
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
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...
Web based servers and softwares for genome analysis
1. Web based servers and softwares for genome analysis
Dr. Naveen Gaurav
Associate Professor and Head
Department of Biotechnology
Shri Guru Ram Rai University
Dehradun
2. Characteristics of Biological Data (Genome Data Management)
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.
Characteristics of Biological Information:
1. There is a high amount and range of variability in data.
There should be a flexibility in biological systems so that it can handle data types and values.
Placing constraints on data types must be limited with such a wide range of possible data
values. There can be a loss of information when there is exclusion of such values.
2. There will be a difference in representation of the same data by different biologists.
This can be done even using the same system. There is a multiple ways to model any given
entity with the results often reflecting the particular focus of the scientist.
There should be a linking of data elements in a network of schemas.
3. Defining the complex queries and also important to the biologists.
Complex queries must be supported by biological systems. Knowledge of the data structure
is needed for the average users because with the help of this knowledge average user can
construct a complex query across data sets on their own. For this systems must provide some
tools for building these queries.
3. 4. When compared with most other domains or applications, biological data becomes
highly complex.
Such data must ensure that no information is lost during biological data modelling and such
data must be able to represent a complex substructure of data as well as relationships. An
additional context is provided by the structure of the biological data for interpretation of
the information.
5. There is a rapid change in schemas of biological databases.
There should be a support of schema evolution and data object migration so that there can
be an improved information flow between generations or releases of databases.
The relational database systems support the ability to extend the schema and a frequent
occurrence in the biological setting.
6. Most biologists are not likely to have knowledge of internal structure of the database or
about schema design.
Users need an information which can be displayed in a manner such that it can be
applicable to the problem which they are trying to address. Also the data structure should
be reflected in an easy and understandable manner. An information regarding the meaning
of the schema is not provided to the user because of the failure by the relational schemas.
A present search interfaces is provided by the web interfaces, which may limit access into
the database.
4. 7. There is no need of the write access to the database by the users of biological data,
instead they only require read access.
There is limitation of write access to the privileged users called curators. There are only
small numbers of users which require write access but a wide variety of read access
patterns are generated by the users into the databases.
8. Access to “old” values of the data are required by the users of biological data most often
while verifying the previously reported results.
Hence system of archives must support the changes to the values of the data in the
database. Access to both the most recent version of data value and its previous version are
important in the biological domain.
9. Added meaning is given by the context of data for its use in biological applications.
Whenever appropriate, context must be maintained and conveyed to the user. For the
maximization of the interpretation of a biological data value, it should be possible to
integrate as many contexts as possible.
5. Web based servers and softwares for genome analysis
Genome browser provides a graphical interface for users to browse, search, retrieve and
analyze genomic sequence and annotation data. Web-based genome browsers can be
classified into general genome browsers with multiple species and species-specific genome
browsers. Currently, there are two types of web-based genome browsers. The first type is the
multiple-species genome browsers implemented in, among others, the UCSC genome
database, the ENSEMBL project, the NCBI Map viewer website, the Phytozome and Gramene
platforms. These genome browsers integrate sequence and annotations for dozens of
organisms and further promote cross-species comparative analysis. Most of them contain
abundant annotations, covering gene model, transcript evidence, expression profiles,
regulatory data, genomic conversation, etc.
1. ENSEMBL (https://asia.ensembl.org/index.html): ENSEMBL is a genome browser for vertebrate
genomes that supports research in comparative genomics, evolution, sequence variation and
transcriptional regulation. ENSEMBL annotate genes, computes multiple alignments, predicts
regulatory function and collects disease data. ENSEMBL tools include BLAST, BLAT, BioMart and
the Variant Effect Predictor (VEP) for all supported species. The Ensembl Rapid Release website
provides annotation for recently produced, publicly available vertebrate and non-vertebrate
genomes from biodiversity initiatives such as Darwin Tree of Life, the Vertebrate Genomes
Project and the Earth BioGenome Project.
Method: a. Open website by the link https://grch37.ensembl.org/index.html
b. Enter the name of living organism (microrganisms, fungi, algae, plants and animals)
c. Enter the obtain sequence (isolated genome from test organism) and compare with data feed in
ensembl tool/website.
6. 2. VISTA: a. Windows Vista, the line of Microsoft Windows client operating systems released
in 2006 and 2007
b. VistA, (Veterans Health Information Systems and Technology Architecture) a medical
records system of the United States Department of Veterans Affairs and others worldwide
c. VISTA (comparative genomics), software tools for genome analysis and genomic sequence
comparisons
d. VistaPro, and Vista, 3D landscape generation software for the Amiga and PC
e. VIsualizing STructures And Sequences, bioinformatics software
Organizations and institutions for VISTA:
1. Vista Entertainment Solutions, a New Zealand software company specializing in solutions for
the cinema industry
2. Americorps VISTA, a national service program to fight poverty through local government
agencies and non-profit organizations
3. Ventura Intercity Service Transit Authorit, a public transportation agency in Ventura County,
California, US
4. Vista Community College, now Berkeley City College, a community college in Berkeley,
California, US
5. Vista Federal Credit Union, now merged with Partners Federal Credit Union, a credit union
that serves employees of The Walt Disney Company
6. Vista University, a now-closed South African university
7. Volunteers in Service to America
8. Vista Equity Partners
9. Vista Oil & Gas, an oil and gas company founded by Miguel Galuccio
10. Vista Outdoor Inc., a U.S.-based publicly traded outdoor and shooting sports compan.
7. 3. UCSC Genome Browser (https://genome.ucsc.edu/): On June 22, 2000, UCSC and the
other members of the International Human Genome Project consortium completed the first working
draft of the human genome assembly, forever ensuring free public access to the genome and the
information it contains. A few weeks later, on July 7, 2000, the newly assembled genome was
released on the web at http://genome.ucsc.edu, along with the initial prototype of a graphical
viewing tool, the UCSC Genome Browser. In the ensuing years, the website has grown to include a
broad collection of vertebrate and model organism assemblies and annotations, along with a large
suite of tools for viewing, analyzing and downloading data. In the years since its inception, the UCSC
Browser has expanded to accommodate genome sequences of all vertebrate species and selected
invertebrates for which high-coverage genomic sequences is available,now including 46 species. High
coverage is necessary to allow overlap to guide the construction of larger contiguous regions.
Genomic sequences with less coverage are included in multiple-alignment tracks on some browsers,
but the fragmented nature of these assemblies does not make them suitable for building full featured
browsers. (more below on multiple-alignment tracks). The species hosted with full-featured genome
browsers are shown in the table.
Browser functionality: The large amount of data about biological systems that is accumulating in the
literature makes it necessary to collect and digest information using the tools of bioinformatics. The
UCSC Genome Browser presents a diverse collection of annotation datasets (known as "tracks" and
presented graphically), including mRNA alignments, mappings of DNA repeat elements, gene
predictions, gene-expression data, disease-association data (representing the relationships of genes
to diseases), and mappings of commercially available gene chips (e.g., Illumina and Agilent). The basic
paradigm of display is to show the genome sequence in the horizontal dimension, and show graphical
representations of the locations of the mRNAs, gene predictions, etc. Blocks of color along the
coordinate axis show the locations of the alignments of the various data types. The ability to show
this large variety of data types on a single coordinate axis makes the browser a handy tool for the
vertical integration of the data.
8. To find a specific gene or genomic region, the user may type in the gene name, a DNA sequence, an
accession number for an RNA, the name of a genomic cytological band (e.g., 20p13 for band 13 on
the short arm of chr20) or a chromosomal position (chr17:38,450,000-38,531,000 for the region
around the gene BRCA1). Presenting the data in the graphical format allows the browser to present
link access to detailed information about any of the annotations. The gene details page of the UCSC
Genes track provides a large number of links to more specific information about the gene at many
other data resources, such as Online Mendelian Inheritance in Man (OMIM) and SwissProt.
Designed for the presentation of complex and voluminous data, the UCSC Browser is optimized for
speed. By pre-aligning the 55 million RNAs of GenBank to each of the 81 genome assemblies (many of
the 46 species have more than one assembly), the browser allows instant access to the alignments of
any RNA to any of the hosted species. The juxtaposition of the many types of data allow researchers
to display exactly the combination of data that will answer specific questions. A pdf/postscript output
functionality allows export of a camera-ready image for publication in academic journals.
One unique and useful feature that distinguishes the UCSC Browser from other genome browsers is
the continuously variable nature of the display. Sequence of any size can be displayed, from a single
DNA base up to the entire chromosome (human chr1 = 245 million bases, Mb) with full annotation
tracks. Researchers can display a single gene, a single exon, or an entire chromosome band, showing
dozens or hundreds of genes and any combination of the many annotations. A convenient drag-and-
zoom feature allows the user to choose any region in the genome image and expand it to occupy the
full screen. Researchers may also use the browser to display their own data via the Custom Tracks
tool. This feature allows users to upload a file of their own data and view the data in the context of
the reference genome assembly. Users may also use the data hosted by UCSC, creating subsets of the
data of their choosing with the Table Browser tool (such as only the SNPs that change the amino acid
sequence of a protein) and display this specific subset of the data in the browser as a Custom Track.
Any browser view created by a user, including those containing Custom Tracks, may be shared with
other users via the Saved Sessions tool.
9. Analysis tools
The UCSC site hosts a set of genome analysis tools, including a full-featured GUI interface for
mining the information in the browser database, a FAST sequence alignment tool BLAT that is
also useful for simply finding sequences in the massive sequence (human genome = 3.23
billion bases [Gb]) of any of the featured genomes.
A liftOver tool uses whole-genome alignments to allow conversion of sequences from one
assembly to another or between species. The Genome Graphs tool allows users to view all
chromosomes at once and display the results of genome-wide association studies (GWAS).
The Gene Sorter displays genes grouped by parameters not linked to genome location, such
as expression pattern in tissues.
4. NCBI genome (https://www.ncbi.nlm.nih.gov/genome/): 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 (NIH). It is approved and funded by the government of
the United States. 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 and is an important resource for bioinformatics tools and
services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic
database for biomedical literature. Other databases include the NCBI Epigenomics database. All
these databases are available online through the Entrez search engine. NCBI was directed by David
Lipman, one of the original authors of the BLAST sequence alignment program and a widely
respected figure in bioinformatics. He also led an intramural research program, including groups
led by Stephen Altschul (another BLAST co-author), David Landsman, Eugene Koonin, John Wilbur,
Teresa Przytycka, and Zhiyong Lu. David Lipman stood down from his post in May 2017.
10. GenBank: NCBI had responsibility for making available the GenBank DNA sequence
database since 1992. GenBank coordinates with individual laboratories and other sequence
databases such as those of the European Molecular Biology Laboratory (EMBL) and
the DNA Data Bank of Japan (DDBJ).
Since 1992, NCBI has grown to provide other databases in addition to GenBank. NCBI
provides Gene, Online Mendelian Inheritance in Man, the Molecular Modeling Database
(3D protein structures), dbSNP (a database of single-nucleotide polymorphisms), the
Reference Sequence Collection, a map of the human genome, and a taxonomy browser,
and coordinates with the National Cancer Institute to provide the Cancer Genome Anatomy
Project. The NCBI assigns a unique identifier (taxonomy ID number) to each species of
organism. The NCBI has software tools that are available through internet browsers or by
FTP. For example, BLAST is a sequence similarity searching program. BLAST can do
sequence comparisons against the GenBank DNA database in less than 15 seconds.
NCBI Bookshelf: The NCBI Bookshelf is a collection of freely accessible, downloadable, on-
line versions of selected biomedical books. The Bookshelf covers a wide range of topics
including molecular biology, biochemistry, cell biology, genetics, microbiology, disease
states from a molecular and cellular point of view, research methods, and virology. Some of
the books are online versions of previously published books, while others, such as Coffee
Break, are written and edited by NCBI staff. The Bookshelf is a complement to the Entrez
PubMed repository of peer-reviewed publication abstracts in that Bookshelf contents
provide established perspectives on evolving areas of study and a context in which many
disparate individual pieces of reported research can be organized.
11. Basic Local Alignment Search Tool (BLAST): BLAST is an algorithm used for calculating sequence
similarity between biological sequences such as nucleotide sequences of DNA and amino acid
sequences of proteins. BLAST is a powerful tool for finding sequences similar to the query sequence
within the same organism or in different organisms. It searches the query sequence on NCBI databases
and servers and posts the results back to the person's browser in the chosen format. Input sequences to
the BLAST are mostly in FASTA or Genbank format while output could be delivered in a variety of formats
such as HTML, XML formatting, and plain text. HTML is the default output format for NCBI's web-page.
Results for NCBI-BLAST are presented in graphical format with all the hits found, a table with sequence
identifiers for the hits having scoring related data, along with the alignments for the sequence of interest
and the hits received with analogous BLAST scores for these.
Entrez: The Entrez Global Query Cross-Database Search System is used at NCBI for all the major
databases such as Nucleotide and Protein Sequences, Protein Structures, PubMed, Taxonomy, Complete
Genomes, OMIM, and several others.[10] Entrez is both an indexing and retrieval system having data from
various sources for biomedical research. NCBI distributed the first version of Entrez in 1991, composed of
nucleotide sequences from PDB and GenBank, protein sequences from SWISS-PROT, translated GenBank,
PIR, PRF, PDB, and associated abstracts and citations from PubMed. Entrez is specially designed to
integrate the data from several different sources, databases, and formats into a uniform information
model and retrieval system which can efficiently retrieve that relevant references, sequences and
structures.[11]
Gene: Gene has been implemented at NCBI to characterize and organize the information about genes. It
serves as a major node in the nexus of the genomic map, expression, sequence, protein function,
structure, and homology data. A unique GeneID is assigned to each gene record that can be followed
through revision cycles. Gene records for known or predicted genes are established here and are
demarcated by map positions or nucleotide sequences. Gene has several advantages over its
predecessor, LocusLink, including, better integration with other databases in NCBI, broader taxonomic
scope, and enhanced options for query and retrieval provided by the Entrez system.[12]
12. Protein database: Protein database maintains the text record for individual protein
sequences, derived from many different resources such as NCBI Reference Sequence
(RefSeq) project, GenBank, PDB, and UniProtKB/SWISS-Prot. Protein records are present in
different formats including FASTA and XML and are linked to other NCBI resources. Protein
provides the relevant data to the users such as genes, DNA/RNA sequences, biological
pathways, expression and variation data, and literature. It also provides the pre-determined
sets of similar and identical proteins for each sequence as computed by the BLAST. The
Structure database of NCBI contains 3D coordinate sets for experimentally-determined
structures in PDB that are imported by NCBI. The Conserved Domain database (CDD of
protein contains sequence profiles that characterize highly conserved domains within
protein sequences. It also has records from external resources like SMART and Pfam. There
is another database in a protein known as Protein Clusters database which contains sets of
proteins sequences that are clustered according to the maximum alignments between the
individual sequences as calculated by BLAST.
Pubchem database:
PubChem database of NCBI is a public resource for molecules and their activities against
biological assays. PubChem is searchable and accessible by Entrez information retrieval
system.
Thank you
References: Online notes, notes from research papers and Books by google search Engine