S.Prasanth Kumar is a bioinformatician who studies proteomics, 2D-PAGE, and proteome databases. Proteomics involves the study of proteins expressed by a genome through analysis of protein sequences, structures, modifications, and interactions. Major databases include Swiss-Prot, which contains annotated protein sequences, and TrEMBL, which contains automatically generated sequences. Other databases contain information on protein families and domains, nucleotide sequences, 2D-PAGE gel images, and post-translational modifications.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
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.
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.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
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.
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.
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
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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.
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.
Archive of experimentally determined 3D structures of biological macromolecules.
Established in 1971, by Research Collaboratory for Structural Bioinformatics (RCSB), Brookhaven National Laboratories, USA.
Archive contain atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structure factors, NMR experimental data.
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
Genomic databases are referred to as online repositories of genomic variants, described for a single (locus-specific) or more (general) genes or specifically for a population or ethnic group (national/ethnic).
INTRODUCTION OF BIOINFORMATICS
HISTORY
WHAT IS DATABASE
NEED FOR DATABASE
TYPES OF DATABASE
PRIMARY DATABASE
NUCLEIC ACID SEQUENCE DATABASE
GENE BANK
INTRODUCTION
GENE BANK SUBMISSION TOOL
GENE BANK SUBMISSION TYPE
HOW TO RETRIEVE DATA FROM GENEBANK
APPLICATION
CONCLUSION
REFERENCE
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
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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.
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.
Archive of experimentally determined 3D structures of biological macromolecules.
Established in 1971, by Research Collaboratory for Structural Bioinformatics (RCSB), Brookhaven National Laboratories, USA.
Archive contain atomic coordinates, bibliographic citations, primary and secondary structure information, crystallographic structure factors, NMR experimental data.
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
Genomic databases are referred to as online repositories of genomic variants, described for a single (locus-specific) or more (general) genes or specifically for a population or ethnic group (national/ethnic).
INTRODUCTION OF BIOINFORMATICS
HISTORY
WHAT IS DATABASE
NEED FOR DATABASE
TYPES OF DATABASE
PRIMARY DATABASE
NUCLEIC ACID SEQUENCE DATABASE
GENE BANK
INTRODUCTION
GENE BANK SUBMISSION TOOL
GENE BANK SUBMISSION TYPE
HOW TO RETRIEVE DATA FROM GENEBANK
APPLICATION
CONCLUSION
REFERENCE
Tutorial on SPARQL 1.1 given at SWAT4LS 2012 in paris to a full room. This material covers enough to get started and includes working with Topbraid Composer.
I presented this PPT presentation during the American Planning Association's Annual Conference in New Brunswick, NJ. It provides some strategies on how to organize your content and identify who your audience is for said target. The presentation has a specific emphasis on how a community planners who seek to obtain community feedback can leverage Social Media to obtain the kinds of feedback they seek for their Grant Reports.
How do people use social media and networking online to search for jobs and advance their careers? We asked nearly 100,000 people from around the world - their responses will surprise you.
Zeel Plast Machinery” established in the year 2013, at Ahmedabad (Gujarat, India), are a prominent Manufacturer, Supplier, Wholesaler and Retailer of highly efficient range of Plastic Containers Blow Moulding Machine, Multi Color Blow Moulding Machine, Toys Blow Moulding Machine, HDPE Blow Moulding Machine.
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.
BITS: Overview of important biological databases beyond sequencesBITS
Module 4 Other relevant biological data sources beyond sequences
Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
INTRODUCTION
DEFINITION OF BIOINFORMATICS
HISTORY
OBJECTIVE OF BIOINFORMATIC
TOOLS OF BIOINFORMATICS
PROCEDURE AND TOOLS OF BIOINFORMATIC
BIOLOGICAL DATABASES
HOMOLOGY AND SIMILARITY TOOLS (SEQUENCE ALIGNMENT)
PROTEIN FUNCTION ANALYSIS TOOLS
STRUCTURAL ANALYSIS TOOLS
SEQUENCE MANIPULATION TOOLS
SEQUENCE ANALYSIS TOOLS
APPLICATION
CONCLUSION
REFERENCES
In the era of computers life sciences databases are still understated. Here is my presentation on biological databases. Complete classification of different databases.
For more presentations and work come and visit
https://www.linkedin.com/in/shradheya-r-r-gupta-54492984/
Information recovery is the recovery of things (objects, Web pages, archives, and so forth) that fulfill explicit conditions set in an ordinary articulation like query. While IR targets fulfilling a bit of client data need generally communicated in common language, information recovery targets figuring out which records contain the specific terms of the user queries.
Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies
S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya
Department of Bioinformatics, ABC, Gujarat University, Ahmedabad- 380009.
Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya. Bioinformatic analysis on Maize sugary1 gene (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Budding Researchers, pp. 173
S. prasanth kumar young scientist awarded presentationPrasanthperceptron
Recipient of Young Scientist Award for Research Article Presentation on “Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein” on an National Symposium on “Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources” held at Department of Botany, Gujarat University, Ahmedabad- 380 009 between Oct 13-15, 2011.
These are the abstracts indexed with my name in the Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources.
1. S.Prasanth Kumar, Bioinformatician Proteomics 2D-PAGE & Proteome Databases S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar FOLLOW ME ON ACCESS MY RESOURCES IN SLIDESHARE prasanthperceptron CONTACT ME [email_address]
3. 2-DE Gel Images Annotated image of Silver stained E.coli 2-DE sample
4. Proteome Proteomics covers the study of the proteins expressed by a genome in a biological sample , such as an organism, an organ, an organelle, a biological fluid Analyze protein sequences for domains and active sites, perform similarity and homology searches, or predict the three-dimensional structure or physico-chemical parameters. Protein sequence, nucleotide sequence, pattern/profile, 2-DE, 3-D structure, PTM, genomic, and metabolic. Databases Types
5. Protein sequence databases SWISS-PROT an annotated universal sequence database, TrEMBL an automatically generated sequence database with repository character, which supplements SWISS-PROT. SWISS-PROT [http://www.expasy.org/sprot/] a curated protein sequence database which provides a high level of annotation Types of Annotations: Description of a protein's function, its domain structure, PTMs, conflicts between literature references and variants. It also provides a minimal level of redundancy , a high level of integration with other bio molecular databases , and an extensive external documentation. (Created in 1986:Main Host-ExPaSy)
6. SWISSPROT format Description Section Reference Section Comments Section
8. Low quality annotations, No SWISSPROT, but trEMBL Genome Sequencing Projects SWISS-PROT annotators, who screen literature and sequence databases Increase in available raw sequence data Automatically populate SWISS-PROT with data of lower quality standards. TrEMBL (Translation of EMBL Nucleotide Sequence Database) Computer-annotated entries in SWISS-PROT-like format . It is populated by protein sequences translated from the coding sequences (CDS) in EMBL and is a supplement to SWISS-PROT
9. Nucleotide sequence databases EBI in Great Britain distributing EMBL Nucleotide Sequence Database, NCBI in the USA distributing GenBank™ , and the NIG in Japan distributing DDBJ Collaboration: EMBL, GenBank and DDBJ all contain the same information (the nucleotide sequence database is in fact one single database distributed under three different names, and in three different formats) Their format is not unified , but they share the same organizational principles as described for SWISS-PROT, i.e. a header containing the name of the sequence, the species of origin, followed by the references, a feature table, and the sequence data. EST to find CDS of gene- dbEST , hosted by NCBI
10. PROSITE regular expression patterns and profiles Pfam HMMs PRINTS fingerprints (groups of aligned, unweighted motifs) Blocks aligned weighted motifs or blocks ProDom is an automatic compilation of homologous domains, derived by clustering of SWISS-PROT and TrEMBL. Databases for protein families, domains and functional sites Above 4 Dbs formed InterPro consortium and developed InterPro , an integrated documentation resource for protein families, domains and functional sites.
11. 2-DE databases Information on proteins identified on 2-DE and consist of two major components: image data and textual information . An image is the representation of a stained gel scanned optically. Apparent spots represent the position of focused protein forms and are linked to the textual information component of the database. Textual information includes, Data on apparent pI and Mw of the spots, the name and description of the protein, the identification method, bibliographical references, and cross- references to SWISS-PROT and other databases.
12. SWISS-2DPAGE The SWISS-2DPAGE database was created and is maintained at the SIB in collaboration with the University Hospital of Geneva. In March 2000, it contained 26 reference maps from human, mouse, Saccharomyces cerevisiae, Escherichia coii and Dictyostellum Discoideum It includes specific fields, such as the type of master gel from which the protein spot has been identified, the list of gel images associated with the entry, as well as other 2-DE specific data, such as the mapping procedure, the spot identifier, the experimental pi and Mw, the peptide mass fingerprint and the amino-acid composition - if experimentally determined.
13. Post-translational modification databases RESID a general database of protein structure modifications (http://www-nbrfgeorgetown.edu/pirwww/dbinfo/resid.html), maintained by the NBRF in the USA and the PIR group The database contains descriptive, chemical, structural, and ibliographical information on 283 (Release 22.1, July 2000) types of modified amino-acid residues. GlycoSuiteDB (http://www.glycosuite.com) is an annotated database of glycan structures. The database is provided by Proteomesystems Ltd and contains information about most published O- and N-linked glycans.
14. O-GLYCBASE , a database of O-glycosylated proteins (http://www.cbs.dtu.dk/databases/OGLYCBASE/), PhosphoBase , a database of phosphorylation sites in proteins and peptides (http://www.cbs.dtu.dk/databases/PhosphoBase/) Both databases are maintained by the Center for Biological Sequence Analysis ( CBS ) in Denmark, which also provides prediction servers for both types of modifications ( NetOGlyc and NetPhos ). Post-translational modification databases