Downloaded 947 times
![PROSITE
Families of proteins
Can search using regular expressions
Similar to unix commands using
wildcards, etc.
E.g., [AC]-x-V-x(4)-{ED}
Interpreted as:
[Ala or Cys]-any-Val-any-any-any-
any-{any but Glu or Asp}
Families exhibit these patterns
So we can search over families
http://ca.expasy.org/prosite/ 22](https://image.slidesharecdn.com/primaryandsecondarydatabasespptupdatedfinal1-170929203851/85/Primary-and-secondary-databases-ppt-by-puneet-kulyana-22-320.jpg)
![PROSITE
Families of proteins
Can search using regular expressions
Similar to unix commands using
wildcards, etc.
E.g., [AC]-x-V-x(4)-{ED}
Interpreted as:
[Ala or Cys]-any-Val-any-any-any-
any-{any but Glu or Asp}
Families exhibit these patterns
So we can search over families
http://ca.expasy.org/prosite/ 22](https://image.slidesharecdn.com/primaryandsecondarydatabasespptupdatedfinal1-170929203851/75/Primary-and-secondary-databases-ppt-by-puneet-kulyana-22-2048.jpg)
Uploaded byPuneet Kulyana
Primary and secondary databases ppt by puneet kulyana
This document provides an introduction to databases used for biological data. It defines key terms like data, information, and databases. It describes different types of biological databases including primary databases that contain original experimental data, and secondary databases that contain derived or analyzed data. Examples of primary databases include GenBank, EMBL, and PDB, while secondary databases include PROSITE, PRINTS, and Pfam that contain conserved protein motifs and families. The document also compares primary and secondary databases.
In this document
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An opening overview of databases and the presentation's structure, including topics like introduction, data, information, and types of databases.
Defines data as raw facts and information as processed data with examples, emphasizing their differences and importance in context.
Categorizes different data types in databases, providing examples like biomolecule sequences and literature databases.
Explains the significance of biological databases in organizing data for meaningful biological analysis.
Introduces primary and secondary databases, setting the stage for detailed discussions in upcoming slides.
Describes primary databases with examples like GenBank and SWISS-PROT which store original bio-molecular data.
Details secondary databases which contain derived data, with examples like PROSITE and Pfam that facilitate protein family analysis.
A comparison of primary and secondary databases, highlighting their roles within biological data management.
List of references that supported the presentation, including course materials and online resources.
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Primary and secondary databases ppt by puneet kulyana
- 1. INTRODUCTION TO DATABASES By:- PUNEET NEERAJ KARTIK VARUN 1
- 2. INDEX/CONTENTS Introduction Data& Information Database Biological Databases Types of Databases - Primary Databases - Secondary Databases - Composite Databases References 2
- 3.
- 4. DATA & INFORMATION DATA Datais raw, unorganized facts that need to be processed. Example:- Each student's test score is one piece of data. INFORMATION When data is processed, organized, structured or presented in a given context so as to make it useful, it is called information. Example:- The average score of a class or of the entire school is information that can be derived from the given data. 4
- 5. DATA INFORMATION Definition (Oxford Dictionaries) Facts andstatistics collected together for reference or analysis Facts provided or learned about something or someone Data as processed, stored, or transmitted by a computer Refers to Raw Data Analyzed Data Description Qualitative Or Quantitative Variables that can be used to make ideas or conclusions A group of data which carries news and meaning In the form of Numbers, letters, or a set of characters. Ideas and inferences Collected via Measurements, experiments, etc. Linking data and making inferences Represented in A structure, such as tabular data, data tree, a data graph, etc. Language, ideas, and thoughts based on the data Interrelation Information that is collected Data that has been processed C O M P A R I S O N B E T W E E N D A T A & I N F O R M A T I O N 5
- 6. S. No. Typeof data Example(s) Weblinks 1. Sequence of biomolecules viz., DNA, RNA, proteins GenBank, EMBL, DDBJ, Swiss-Prot, PIR (i) www.ncbi.nlm.nih.gov/genba nk/ (ii) https://www.ebi.ac.uk/embl/ (iii) www.ddbj.nig.ac.jp/ (iv)http://web.expasy.org/docs/s wiss-prot_guideline.html (v) http://pir.georgetown.edu/ 2. Bio-molecular structures PDB http://www.rcsb.org/pdb/home /home.do 3. Bibliography/scientific literature ** PubMed, Scopus (Search engine) (i) www.ncbi.nlm.nih.gov/pubme d (ii) www.scopus.com 4. Patent databases USPTO www.uspto.gov/ 5. Metabolic pathways / molecular interactions KEGG http://www.genome.jp/kegg/pa thway.htm 6 TYPES OF DATA & INFORMATION Databases are categorized based on the data type. A few examples are listed below:-
- 7. DATABASE??? A database isa collection of data in an organized manner, which is accessible in various ways. 7
- 8. WHAT ARE THEBIOLOGICAL DATABASES ??? 8
- 9. Biological Databases servea critical purpose in the collation and organization of data related to biological systems. They provide a computational support and a user-friendly interface to a researcher for a meaningful analysis of biological data. 9
- 10. TYPES OF DATABASES Primary Databases Secondary Databases 10
- 11. PRIMARY DATABASES Containsbio-molecular data in its original form. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Once given a database accession number, the data in primary databases are never changed. Examples :- GenBank, EMBL and DDBJ for DNA/RNA sequences, SWISS-PROT and PIR for protein sequences and PDB for molecular structures. 11
- 12. GenBank Database from NCBI,includes sequences from publicly available resources. http://www.ncbi.nlm.nih.gov/genbank/ 12
- 13. EMBL European MolecularBiological Laboratory Nucleic acid database from EBI (European Bioinformatics Institute) Produced in collaboration with DDBJ and GenBank Search engine – SRS (Sequence Retrieval System) http://www.ebi.ac.uk/ 13
- 14. DDBJ DNA Databankof Japan Started in 1986 in collaboration with GenBank Produced and maintained at NIG (National Institute of Genetics) http://www.ddbj.nig.ac.jp/ 14
- 15. SWISS PROT Annotatedsequence database established in 1986 Consists of sequence entries of different lie formats Similar format to EMBL http://us.expasy.org/sprot/sprot-top.html http://www.ebi.ac.uk/uniprot/ 15
- 16. PIR Protein InformationResource A division of National Biomedical Research Foundation (NBRF) in U.S. One can search for entries or do sequence similarity search at PIR site. http://pir.georgetown.edu/ 16
- 17. TrEMBL Translated EuropeanMolecular Biology Laboratory Computer annotated supplement of SWISS PROT. Contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS PROT. http://www.ebi.ac.uk/trembl/ 17
- 18. COMPOSITE DATABASES Collectionof various primary database sequences Renders sequence searching highly efficient as it searches multiple resources Examples :- NRDB (Non Redundant Database), OWL, MIPSX, SWISS PROT + TrEMBL 18
- 19.
- 20. SECONDARY DATABASES Containsdata derived from the results of analysing primary data Manually created or automatically generated Contains more relevant and useful information structured to specific requirements Example :- PROSITE, PRINTS, BLOCKS, Pfam 20
- 21. SECONDARY DATABASES SECONDARY DATABASE PRIMARY SOURCE INFORMATION STORED PROSITE SWISSPROT Regular expression BLOCKS PROSITE/PRIN TS Aligned motifs(blocks) PRINTS OWL (Composite DB) Aligned motifs Pfam SWISS PROT Hidden Markov Models Profile SWISS PROT Weighted Matrices(profile) 21
- 22. PROSITE Families of proteins Cansearch using regular expressions Similar to unix commands using wildcards, etc. E.g., [AC]-x-V-x(4)-{ED} Interpreted as: [Ala or Cys]-any-Val-any-any-any- any-{any but Glu or Asp} Families exhibit these patterns So we can search over families http://ca.expasy.org/prosite/ 22
- 23. BLOCKS Motifs/blocks are created by automatically detectingthe most conserved regions of each protein family. 23
- 24. PRINTS Most proteinfamilies are characterized not by one, but by several conserved motifs Fingerprints are groups of conserved motifs excised from sequence alignments Taken together, they provide diagnostic family signatures. They are the basis of the PRINTS database, and are stored in the form of aligned motifs. Input about protein families is done manually 24
- 25. Pfam Maintained by theSanger Centre (Cambridge) Protein families aligned using HMMs Hidden Markov Models Given a new sequence Find families which the sequence might fit into Sequence Coverage 11912 families Split into Pfam-A (high quality) and Pfam-B (low quality) http://pfam.sanger.ac.uk/ 25
- 26.
- 27. PRIMARY VS SECONDARYDATABASES 27
- 28. REFERENCES Class notes ESSENTIAL BIOINFORMATICS- Jin Xiong file:///C:/Users/student/Downloads/DATABASES%2 0IN%20BIOINFORMATICS.pdf https://www.ebi.ac.uk/training/online/course/bioinfor matics-terrified/what-database/relational- databases/primary-and-secondary-databases http://www.diffen.com/difference/Data_vs_Informa tion Google images 28
- 29.