Clustal Omega is a fast and scalable program for multiple sequence alignment. It begins by producing pairwise alignments using a word-based heuristic method. It then clusters the sequences using a modified mBed distance method and k-means clustering. Finally, it generates the multiple sequence alignment using the HHAlign package, which aligns profile HMMs built from the sequences. Clustal Omega is widely considered one of the fastest online multiple sequence alignment tools.
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:
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:
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.
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
Global and local alignment (bioinformatics)Pritom Chaki
A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
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.
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
This presentation entitled 'Molecular phylogenetics and its application' deals with all the developmental ideas and basics in the field of bioinformatics.
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.
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.
Clustal omega is a widely used bioinformatics tool for performing multiple sequence alignment. This ppt contains the concept and types of sequence alignment, algorithms followed by clustal omega, its result interpretation and applications.
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.
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
Global and local alignment (bioinformatics)Pritom Chaki
A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
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.
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
This presentation entitled 'Molecular phylogenetics and its application' deals with all the developmental ideas and basics in the field of bioinformatics.
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.
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.
Clustal omega is a widely used bioinformatics tool for performing multiple sequence alignment. This ppt contains the concept and types of sequence alignment, algorithms followed by clustal omega, its result interpretation and applications.
https://github.com/telecombcn-dl/dlmm-2017-dcu
Deep learning technologies are at the core of the current revolution in artificial intelligence for multimedia data analysis. The convergence of big annotated data and affordable GPU hardware has allowed the training of neural networks for data analysis tasks which had been addressed until now with hand-crafted features. Architectures such as convolutional neural networks, recurrent neural networks and Q-nets for reinforcement learning have shaped a brand new scenario in signal processing. This course will cover the basic principles and applications of deep learning to computer vision problems, such as image classification, object detection or text captioning.
International Refereed Journal of Engineering and Science (IRJES)irjes
The core of the vision IRJES is to disseminate new knowledge and technology for the benefit of all, ranging from academic research and professional communities to industry professionals in a range of topics in computer science and engineering. It also provides a place for high-caliber researchers, practitioners and PhD students to present ongoing research and development in these areas.
An Empirical Study for Defect Prediction using Clusteringidescitation
Reliably predicting defects in the software is one of
the holy grails of software engineering. Researchers have
devised and implemented a method of defect prediction
approaches varying in terms of accuracy, complexity, and the
input data they require. An accurate prediction of the number
of defects in a software product during system testing
contributes not only to the management of the system testing
process but also to the estimation of the product’s required
maintenance [1]. A prediction of the number of remaining
defects in an inspected artefact can be used for decision making.
Defective software modules cause software failures, increase
development and maintenance costs, and decrease customer
satisfaction. It strives to improve software quality and testing
efficiency by constructing predictive models from code
attributes to enable a timely identification of fault-prone
modules [2]. In this paper, we will discuss clustering techniques
are used for software defect prediction. This helps the
developers to detect software defects and correct them.
Unsupervised techniques may be used for defect prediction in
software modules, more so in those cases where defect labels
are not available [3].
Parallel and distributed genetic algorithm with multiple objectives to impro...khalil IBRAHIM
we argue that the timetabling problem reflects the problem of scheduling university courses, So you must specify the range of time periods and a group of instructors for a range of lectures to check a set of constraints and reduce the cost of other constraints ,this is the problem called NP-hard, it is a class of problems that are informally, it’s mean that necessary operations to solve the problem will increase exponentially and directly proportional to the size of the problem, The construction of timetable is the most complicated problem that was facing many universities, and increased by size of the university data and overlapping disciplines between colleges, and when a traditional algorithm (EA) is unable to provide satisfactory results, a distributed EA (dEA), which deploys the population on distributed systems, it also offers an opportunity to solve extremely high dimensional problems through distributed coevolution using a divide-and-conquer mechanism, Further, the distributed environment allows a dEA to maintain population diversity, thereby avoiding local optima and also facilitating multi-objective search, by employing different distribution models to parallelize the processing of EAs, we designed a genetic algorithm suitable for Universities environment and the constraints facing it when building timetable for lectures.
Clonal Selection Algorithm Parallelization with MPJExpressAyi Purbasari
This paper exploits the parallelism potential on a Clonal Selection Algorithm (CSA) as a parallel metaheuristic algorithm, due the lack of explanation detail of the stages of designing parallel algorithms. To parallelise population-based algorithms, we need to exploit and define their granularity for each stage; do data or functional partition; and choose the communication model. Using a library for a message-passing model, such as MPJExpress, we define appropriate methods to implement process communication. This research results pseudo-code for the two communication message-passing models, using MPJExpress. We implemented this pseudo-codes using Java Language with a dataset from the Travelling Salesman Problem (TSP). The experiments showed that multicommunication model using alltogether method gained better performance that master-slave model that using send-and receive method.
Clustering and Classification Algorithms Ankita DubeyAnkita Dubey
Clustering is a process of partitioning a set of data (or objects) into a set of meaningful sub-classes, called clusters. Help users understand the natural grouping or structure in a data set. Used either as a stand-alone tool to get insight into data distribution or as a preprocessing step for other algorithms.
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.
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.
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.
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.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
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.
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
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.
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.
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.
6. Multiple Alignment Method
• The steps are summarized as follows:
• Compare all sequences pairwise.
• Perform cluster analysis on the pairwise data to generate a
hierarchy for alignment. This may be in the form of a binary tree
or a simple ordering
• Build the multiple alignment by first aligning the most similar
pair of sequences, then the next most similar pair and so on. Once
an alignment of two sequences has been made, then this is fixed.
Thus for a set of sequences A, B, C, D having aligned A with C and
B with D the alignment of A, B, C, D is obtained by comparing the
alignments of A and C with that of B and D using averaged scores
at each aligned position.
7. ClustalW- for multiple alignment
• ClustaW is a general purpose multiple alignment
program for DNA or proteins.
• ClustalW is produced by Julie D. Thompson, Toby
Gibson of European Molecular Biology Laboratory,
Germany and Desmond Higgins of European
Bioinformatics Institute, Cambridge, UK. Algorithmic
• ClustalW is cited: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting,
positions-specific gap penalties and weight matrix choice.
Nucleic Acids Research, 22:4673-4680.
8. ClustalW can create multiple alignments,
manipulate existing alignments, do profile
analysis and create phylogentic trees.
Alignment can be done by 2 methods:
- slow/accurate
- fast/approximate
15. Clustal X - Multiple Sequence
Alignment Program
• Clustal X provides a new window-based user interface to the
ClustalW program.
• It uses the Vibrant multi-platform user interface development
library, developed by the National Center for Biotechnology
Information (Bldg 38A, NIH 8600 Rockville Pike,Bethesda, MD
20894) as part of their NCBI SOFTWARE DEVELOPEMENT
TOOLKIT.
21. Fast and scalable program written in C and C++ used
for multiple sequence alignment.
It uses seeded guide trees and a
new HMM engine that focuses on two
profiles to generate these alignments.
The program requires three or more
sequences in order to calculate
the multiple sequence alignment, for
two sequences use pairwise sequence
alignment tools (EMBOSS, LALIGN).
Clustal Omega is consistency-based
and is widely viewed as one of the
fastest online implementations of all
multiple sequence alignment tools and
CLUSTAL OMEGA
22. shown here.
Clustal Omega has five main steps .
The first is producing a pairwise alignment using
the k-tuple method, also known as the word
method. This, in summary, is a heuristic method
to find an optimal alignment solution, but is
significantly more efficient than the dynamic
programming method of alignment. After that,
the sequences are clustered using the modified
mBed method. The mBed method calculates
pairwise distance using sequence embedding.
This step is followed by the k-means clustering
method.
ALGORITHM
23. method. This is shown as multiple guide tree steps
leading into one final guide tree construction because
of the way the UPGMA algorithm works.
At each step, (each diamond in the flowchart) the
nearest two clusters are combined and is repeated until
the final tree can be assessed. In the final step,
the multiple sequence alignment is produced using
HHAlign package from the HH-Suite, which uses two
profile HMM's.
A profile HMM is a linear state machine consisting of a
series of nodes, each of which corresponds roughly to a
position (column) in the alignment from which it was
built
