This document discusses key concepts in comparative genomics including orthologs, paralogs, speciation, and clusters of orthologous genes (COGs). It defines orthologs as genes evolved from a common ancestor through speciation that retain the same function, while paralogs are related through duplication and may evolve new functions. COGs are groups of orthologous genes from different species that are more similar to each other than to other genes within individual genomes. The document notes that COGs can be used to predict gene function and track evolutionary divergence. It provides an example of the NCBI COG database containing over 136,000 proteins from 50 bacteria, 13 archaea and 3 eukaryotes classified into CO
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
Functional proteomics, methods and toolsKAUSHAL SAHU
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
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.
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
Comparative genomics in eukaryotes, organellesKAUSHAL SAHU
WHAT IS COMPARATIVE GENOMICS?
HISTORY
SOME RELATED TERMS
MINIMAL EUKARYOTIC GENOMES
COMPARISON OF THE MAJOR SEQUENCED GENOMES
EUKARYOTIC GENOMES
SACCHAROMYCES CEREVISIAE GENOME
INSECT GENOME
DROSOPHILA MELANOGASTER (FRUIT FLY) GENOME
COMPARATIVE ANALYSIS OF THE HUMAN AND MOUSE GENOME
COMPARATIVE GENOMICS OF ORGANELLES
COMPARATIVE GENOMICS TOOLS
CONCLUSION
REFERENCES
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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.
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
Functional proteomics, methods and toolsKAUSHAL SAHU
INTRODUCTION
HISTORY
DEFINITION
PROTEOMICS
FUNCTIONAL PROTEOMICS
PROTEOMICS SOFTWARE
PROTEOMICS ANALYSIS
TOOLS FOR PROTEOM ANALYSIS
DIFFERENTS METHODS FOR STUDY OF FUNCTIONAL PROTEOMICS
APLLICATIONS
LIMITATIONS
CONCLUSION
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
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.
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
Comparative genomics in eukaryotes, organellesKAUSHAL SAHU
WHAT IS COMPARATIVE GENOMICS?
HISTORY
SOME RELATED TERMS
MINIMAL EUKARYOTIC GENOMES
COMPARISON OF THE MAJOR SEQUENCED GENOMES
EUKARYOTIC GENOMES
SACCHAROMYCES CEREVISIAE GENOME
INSECT GENOME
DROSOPHILA MELANOGASTER (FRUIT FLY) GENOME
COMPARATIVE ANALYSIS OF THE HUMAN AND MOUSE GENOME
COMPARATIVE GENOMICS OF ORGANELLES
COMPARATIVE GENOMICS TOOLS
CONCLUSION
REFERENCES
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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.
Slides from a Comparative Genomics and Visualisation course (part 2) presented at the University of Dundee, 11th March 2014. Other materials are available at GitHub (https://github.com/widdowquinn/Teaching)
This is the first presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on different levels.
Thanks to Klaas Vandepoele of the PSB department.
Molecular Systematics provides a solid conceptual basis for the evolutionary history of organisms. Molecular systematics is the study of DNA and RNA sequences to infer evolutionary links across organisms. Molecular approaches/ techniques provide excellent resources for the study of evolution and phylogeny.
This slide contains the detailed information of bhageerath H tool for homology modelling (for tertiary structure prediction) designed by SCFBio, IIT Delhi.
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.
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Bills have a main role in point of sale procedure. It will help to track sales, handling payments and giving receipts to customers. Bill splitting also has an important role in POS. For example, If some friends come together for dinner and if they want to divide the bill then it is possible by POS bill splitting. This slide will show how to split bills in odoo 17 POS.
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.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
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.
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
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!
2. Some important terminologies:
Orthologs are genes in different species that evolved from a
common ancestral gene by speciation. Normally, orthologs retain the
same function in the course of evolution. Identification of orthologs
is critical for reliable prediction of gene function in newly sequenced
genomes.
Paralogs are genes related by duplication within a genome.
Orthologs retain the same function in the course of evolution,
whereas paralogs evolve new functions, even if these are related to
the original one.
Speciation is the origin of a new species capable of making a living
in a new way from the species from which it arose. As part of this
process it has also acquired some barrier to genetic exchange with
the parent species.
4. COGs
• Cluster of orthologous genes.
• Clusters of Orthologous Groups, are groups of three or more ortholog
genes, meaning they are direct evolutionary counter parts and are
considered to be part of an 'ancient conserved domain'. A COG is defined
as three or more proteins from the genomes of distant species that are
more similar to each other than to any other protein within the individual
genome.
• COGs can be used to predict the function of homologous proteins in
poorly studied species and can also be used to track the evolutionary
divergence from a common ancestor, hence providing a powerful tool for
functional annotation of uncharacterized proteins.
• Important in comparative genomics studies
5. Application of COG
• The most straightforward application of the COGs is for the prediction of
functions of individual proteins or protein sets, including those from newly
completed genomes.
NCBI provides a COG database that consists of 4,873 COGs that code for over
136,000 proteins from the genomes of 50 bacteria, 13 archaea and 3 unicellular
eukaryotes. This database uses completely sequenced genomes to classify
proteins using the orthology concept.
The COG database
6. What are some questions that comparative
genomics can address?
• How has the organism evolved?
• What differentiates species?
• Which non-coding regions are important?
• Which genes are required for organisms to survive in a
certain environment?
7. What is Comparative Genomics?
It is the comparison of one genome to another.
Genomics DNA (Gene)
Functional
Genomics
Transcriptomics RNA
Proteomics PROTEIN
Metabolomics METABOLITE
Transcription
Translation
Enzymatic
reaction
8. Difference is in Scale and Direction
One or several genes
compared against all
other known genes.
Use genome to
inform us about the
entire organism.
Use information
from many
genomes to learn
more about the
individual genes.
Entire Genome
compared to
other entire
genomes.
Other “omics” Comparative
9. Comparative genomics
• Discover what lies hidden in genomic
sequence by comparing sequence
information.
• Main areas
– Whole genome alignment
– Gene prediction
– Regulatory element prediction
– Phylogenomics
– Pharmacogenetics
10. Comparative Genomics
Comparative genomics is a powerful tool for identifying the features and dissecting
the functions of genomes. The approach is based on selection for the gene or
regulatory region constraining the evolution of the sequence. Comparison with other
genomes has become an integral part of the analysis of the human genome sequence
and is one of the most effective methods for identifying genes (Batzoglou et al. ,
2000; Roest Crollius et al. , 2000)
Comparative genomics is a field of biological research in which the genomic features of
different organisms are compared. The genomic features may include the DNA sequence,
genes, gene order, regulatory sequences, and other genomic structural landmarks
13. Figure: Distribution and clustering of orthologous genes of Tulsi genome to other related plant
genomes. a. Distribution of gene families among five plant genomes. Ocimum tenuiflorum (Ote
- green), Arabidopsis thaliana (Ath – black rectangle), Oryza sativa (Osa – red), Solanum
lycopersicum (Sly – blue) and Mimulus guttatus (Mgu – black circle). The numbers in the Venn
diagram represent shared and unique gene families across these 5 species obtained by
OrthoMCL.
b. Horizontal stacked bar plot of all the genes in 23 different genomes. This figure shows
ortholog group distribution in all 23 plant species including Tulsi. Each row represents a plant
species - Physcomitrella patens (Ppa), Selaginella moellendorffii (Smo), Oryza sativa (Osa),
Setaria italic (Sit), Zea mays (Zma), Sorghum bicolor (Sbi), Aquilegia caerulea (Aca), Ocimum
tenuiflorum (Ote), Mimulus guttatus (Mgu), Solanum lycopersicum (Sly), Solanum tuberosum
(Stu), Vitis vinifera (Vvi), Eucalyptus grandis (Egr), Citrus sinensis (Csi), Theobroma cacao (Tca),
Carica papaya (Cpa), Brassica rapa (Bra), Arabidopsis thaliana (Ath), Fragaria vesca (Fve), Prunus
persica (Ppe), Glycine max (Gma), Medicago truncatula (Mtr), Populus trichocarpa (Ptr). The bar
graph represents ortholog protein groups for that species subdivided into 22 categories
depending on the degree of sharing with the other 22 plant species e.g., category 2 represents
the number of orthologous groups that have representatives from the species of interest and
from one more species out of the 23 species selected for the study
14. Background: Shortly after multiple
genome sequences of bacteria, archae
and unicellular eukaryotes became
available, an attempt on such a
classification was implemented in
Cluster of Orthologous Groups of
proteins (COGs). Rapid accumulation of
genome sequences creates
opportunities for refining COGs but also
represents a challenge because of error
amplification.
Conclusion: The arCOGs provide a
convenient, flexible framework for
functional annotation of archael
genomes, comparative genomics and
evolutionary reconstructions. Genomic
reconstructions suggest that the last
common ancestor of archaea might
have been (nearly) as advanced as the
modern archael hyperthermophiles.
For more info:
ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/.
15.
16. MBGD Database
MBGD is a database for comparative analysis of completely sequenced microbial
genomes, the number of which is now growing rapidly. The aim of MBGD is to
facilitate comparative genomics from various points of view such as ortholog
identification, paralog clustering, motif analysis and gene order comparison.
17. Conclusion
The study of Cluster of Orthologous
Genes play a vital role in the
Comparative genomic studies.
18. References and links
• NCBI COGs database
• Chapter 22 of the NCBI handbook: The Clusters of Orthologous Groups (COGs)
Database: Phylogenetic Classification of Proteins from Complete Genomes. NCBI
Bookshelf ID: NBK21101.
• NCBI News Letter: Protein Families and Genome Evolution. Published Feb 1998.
• http://homepage.usask.ca/~ctl271/857/def_homolog.shtml
• http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-2-33
• Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223.
Epub 2014 Nov 26.
• http://www.ncbi.nlm.nih.gov/pubmed/25428365
• http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-2-33
Homology: Is the relationship between biological structures or sequences that are derived from a common ancestry.
Two things are homologous if they bear same relationship to one another, such as a certain bone in various forms of the “hand”.
