Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
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.
Secondary Structure Prediction of proteins Vijay Hemmadi
Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
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.
Secondary Structure Prediction of proteins Vijay Hemmadi
Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
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.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
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.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
Standardized visualisation of differences between model versionsVasundra Touré
Visualising differences in SBML models using SBGN and BiVeS
Tom Gebhardt, Martin Scharm, Vasundra Toure, Dagmar Waltemath, Olaf Wolkenhauer
University of Rostock
Talk given during COMBINE 2016 in Newcastle upon Tyne, the 24th of September 2016.
Talk by Martin Scharm at the COMBINE meeting September 2013 in Paris.
Find more information and download the slides at http://sems.uni-rostock.de/2013/09/sems-at-the-combine-2013/
ADMET properties prediction using AI will accelerate the process of drug discovery.
This slide mostly focuses on using graph-based deep learning techniques to predict drug properties.
In this video from the 2015 HPC User Forum in Broomfield, Barry Bolding from Cray presents: HPC + D + A = HPDA?
"The flexible, multi-use Cray Urika-XA extreme analytics platform addresses perhaps the most critical obstacle in data analytics today — limitation. Analytics problems are getting more varied and complex but the available solution technologies have significant constraints. Traditional analytics appliances lock you into a single approach and building a custom solution in-house is so difficult and time consuming that the business value derived from analytics fails to materialize. In contrast, the Urika-XA platform is open, high performing and cost effective, serving a wide range of analytics tools with varying computing demands in a single environment. Pre-integrated with the Hadoop and Spark frameworks, the Urika-XA system combines the benefits of a turnkey analytics appliance with a flexible, open platform that you can modify for future analytics workloads. This single-platform consolidation of workloads reduces your analytics footprint and total cost of ownership."
Learn more: http://www.cray.com/products/analytics/urika-xa
Watch the video presentation: http://wp.me/p3RLEV-3yR
Sign up for our insideBIGDATA Newsletter: http://insidebigdata.com/newsletter
3D printing & open access databases for crystallographic college educationVincent Scalfani
Moeck, P.; Stone-Sundberg, J.; Snyder, T.J.; Kaminsky, W.; Gražulis, S.; and all members of the International Advisory Board of the Crystallography Open Database. In 3D printing & open access databases for crystallographic college education, IUCr 23rd Congress on Crystallography, Montreal, Canada, 2014.
Peptide vaccine containing only epitopes capable of inducing positive, desirable T cell and B cell mediated immune response.
Peptides‖ used in these vaccines are 20–30 amino acid sequences that are synthesized to form an immunogenic peptide molecule representing the specific epitope of an antigen.
sufficient for activation of the appropriate cellular and humoral responses
Eliminating allergenic and/or reactogenic responses.
The different types of external stresses that influence the plant growth and development.
These stresses are grouped based on their characters
Biotic
Abiotic
Almost all the stresses, either directly or indirectly, lead to the production of reactive oxygen species (ROS) that create oxidative stress in plants.
This damages the cellular constituents of plants which are associated with a reduction in plant yield.
Bioreactors are devices in which biological or biochemical processes develop under a closely monitored and tightly controlled environment. Bioreactors have been used in animal cell culture since the 1980s in order to produce vaccines and other drugs and to culture large cell populations. Bioreactors for use in tissue engineering have progressed from such devices.
A tissue engineering bioreactor can be defined as a device that uses mechanical means to influence biological processes. In tissue engineering, this generally means that bioreactors are used to stimulate cells and encourage them to produce extracellular matrix (ECM). There are numerous types of bioreactor which can be classified by the means they use to stimulate cells.
Microgravity is the condition in which people or objects appear to be weightless (In space). Astronauts and cosmonauts returning from long-term space missions exhibited various health problems, among them changes of the immune system, bone loss, muscle atrophy, ocular problems, and cardiovascular changes. Space biologists investigated various cell types in space to find the molecular mechanisms responsible for the observed immune disorders. Experimental cell research studying three-dimensional (3D) tissues in space and on Earth using new techniques to simulate microgravity is currently a hot topic in Gravitational Biology and Biomedicine.
An idea was considered as to producing an entire organ in vivo by bypassing many of the steps like cell isolation and expansion, culturing in bioreactors, scaffolds and growth factor delivery ect. involved in traditional tissue engineering. This concept was called the in vivo bioreactor (IVB).
Biomaterials were defined as “any substance, other than a drug, or a combination of substances, synthetic or natural in origin, which can be used for any period of time, as a whole or as a part of a system, which treats, augments or replaces any tissue, organ or function of the body”
Hematopoiesis is the process through which the body manufactures blood cells. It begins early in the development of an embryo, well before birth, and continues for the life of an individual. Hematopoiesis begins during the first weeks of embryonic development. All blood cells and plasma develop from a stem cell that can develop into any other cell.
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
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.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
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
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
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.
1. Department of Zoology, GACW (2018-2019)
Protein structure visualization tools
Introduction:
Before computer visualization software was developed, molecular structures
were presented by physical models of metal wires, rods and spheres. With
the development of computer hardware and software technology and
computer graphics programs were developed to visualizing and
manipulating three-dimensional structures. The computer graphics help to
analyze and compare protein structure to gain the functions of protein.
Molecular visualization helps the scientists to bioengineer the protein
molecules. User-friendly graphic interface makes this area of
Bioinformatics a full filled, scientific thrill to the bioscientists.
Tools for molecular visualization:
There are a number of software’s both free and commercial are available to
visualize the biomolecules. The most commonly used free software are :
RasMol
Chime
MolMol
Protein explorer
Kinemage Cn3D
RasMol
RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules. It is created by Roger Sayle in
1992. The program is aimed at display, teaching and generation of publication
quality images. RasMol runs on wide range of architectures and operating
systems including Microsoft Windows, Apple Macintosh, UNIX and VMS
systems.
2. Department of Zoology, GACW (2018-2019)
Link for RasMol : http://www.openrasmol.org/#features_rasmol
RasMol Features:
The program consists of two windows:
For the command line
For providing the graphics.
1. Input file format:
The input file can be in PDB format and can be downloaded from the
PDB structure database.
Protein Data Bank (PDB) files can be downloaded for visualization
from members of the Worldwide Protein Data Bank (wwPDB). These
have been uploaded by researchers who have characterized the
structureof molecules usually by X-ray crystallography, protein NMR
spectroscopy, or cryo-electron microscopy.
3. Department of Zoology, GACW (2018-2019)
2. Display:
There are different ways of displaying coordinates. These include:-
wireframe, sticks, spacefill, strands & cartoons.
The initial image is shown as a „wire” model.
-from the Display menu one can choose other
visualisation styles such as „spacefill”, „stick”, „ball and
stick” as well as the visually most attractive „ribbon” and
„cartoon” models.
In the last two styles, alpha helices are rendered as helical ribbons and
beta structures as flat arrows pointing in the direction of the
polypeptide chain.
3. Colour:
The atoms of the model can be coloured by the standard CPK (named
after Corey, Pauling and Koltun)
To color by atom type : Colours/CPK
4. Department of Zoology, GACW (2018-2019)
Carbon: gray
Hydrogen: white
Oxygen: red
Nitrogen: blue
Sulfur: yellow
Iron: yellow
The protein can be coloured based on polypeptide chains, the
chemical property of the amino acids.
To color by the protein-secondary structure: Colours/Structure
-helices: magenta
-sheets: yellow
turns: pale blue
all other residues: white
The structure can be cut in the z-dimension
The left and right mouse buttons can be used to rotate the protein along
the „x” and „y” axes.
4. For moving the molecule(s):
Action PC
Rotation Left-mouse
button (Click & Hold)
Translation Right-mouse
button (Click & Hold)
Zoom <alt><SHIFT> and
left-mouse button
Z-Rotation <alt><SHIFT>and
right-mouse button
5. Atom Selection and view:
By clicking any part of the structure, the residue number of the given
chain and the particular atom will be shown in the command window.
5. Department of Zoology, GACW (2018-2019)
One can select a chain, a particular residue or segment of the chain by
using the „select” command. „Select 25A” in the command window
means that the 25th residue of chain A will be selected.
The name of the residue can also be used. A segment of a chain can also
be selected: for example, „select 1-33” means that the first 33 residues of
the chain will be selected.
If the structure contains a ligand (coenzyme, substrate, metal ion etc.)
besides the polypeptide chain, it can be selected by the „hetero”
command or by its name (e.g. „ca” refers to a Ca2+
ion).
The background of the image can be set by the „background color”
syntax.
If we want to remove part of the structure, it can be done by using the
„restrict” command (e.g. „restrict 1-56” will remove the rendering of the
chain from residue 57 to the C-terminal end).
One can save the modified structure (e.g. for later manipulation) by the
„write script” command and a file name.
The finished structure can be saved in common graphics file formats
(gif, jpeg, etc.).
The „help” menu can explain many additional commands that can be
used to manipulate the structure.
References:
http://www.chemistry.wustl.edu/~edudev/rasdir.html
https://www.bioch.ox.ac.uk/www-courses/molecular_graphics/
https://slideplayer.com/slide/11477823/