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BIOLOGICAL SEQUENCE DATABASES
The document discusses the National Center for Biotechnology Information (NCBI), which maintains biological databases and provides bioinformatics tools. NCBI houses both primary databases directly submitted by researchers and secondary databases compiled from primary sources. Major databases include GenBank (nucleotide sequences), PubMed Central (biomedical literature), and reference sequence databases. Tools like BLAST, Entrez, and ORFfinder allow users to search and analyze sequence data. NCBI aims to make biomedical research data freely accessible worldwide.
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BIOLOGICAL SEQUENCE DATABASES
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- 2. NCBI What isNCBI? National center for biotechnology information Established in 1998 Part of national library of medicine at national institute of health Major aim : public database Development of software tools for sequence analysis and disseminate biomedical information 2
- 3. 2 explain Rolesof NCBI 1) Maintenance of biological databases whether primary or secondary. It includes GENEBANK 2) NCBI provides the data retrieval systems such as ENTREZ 3) Provides computational sources for the analysis of the GENEBANK data and other biological data 3
- 4. Kinds of databases Primarydatabases Secondary databases Original submission by the experimentalists who have originally searched Content Is controlled by the submitters Examples include GENEBANK, SNP and GEO Built up from primary data which is retrieved by primary database Content controlled by third party NCBI Examples include RefSeq, RefSNP, NCBI Structure, Protein. Etc. 4
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- 6. 6 NCBI TOOLS BLAST Standard blast Megablast PSI-blast PHI-blast RPS blast BLAST 2 SEQ DATABASE RETREIVAL TOOL SPECIALIZED TOOL ORF finder E-pcr Sequence submission tool bankit Spidey DATABASES Nucleotide database Literature database Protein database Expression database Structure database
- 7. Retrieval tool ENTREZ Integrated database search and retrieval system Provides extensive links between and within database records Cross references of different databases 7
- 8. 3 Sequence submissionto NCBI Databases are constantly updated with the newer submissions of the sequences via sequence submission tools such as: Bankit Sequein 8
- 9. Bank it Web-basedsequence submission tool Connect to NCBI Home Page Connect to GENEBANK side bar at left Tool of choice for simple submissions Can also be used for updating previously added information 9
- 10. Sequein Stand alonesequence submission and updating tool Handling multiple sequence submission Provides increased capacity for long sequence submissions Multiple annotation Phylogenetic analysis population 10
- 11. BLAST Basic localalignment search tool program Sequence similarity searches against a variety of different sequence databases Unigene, gene, MMDB, GEO 11
- 12. Kinds of BLAST 12 BlastnBlastp Blastx Tblastn Tblastx
- 13. SPECIALIZED TOOLS Thereare a lot of sequence analysis tools which will be explained later 1) ORF Finder 2) e-PCR 3) SPIDEY 13
- 14. ORF FINDER Openreading frame finder Graphical analysis tool Finds all open reading frames in the user’s sequence or the sequence already submitted in the databases Uses standard and alternative genetic codes for the analysis of reading frames Packaged with sequein 14
- 15. e-PCR Electronic polymerasechain reaction Searches for the STS Whole template DNA is searched for STS New database searches a query sequence against a sequence database 15
- 16. Spidey This isanother m RNA to genome alignment tool Searches databases via BLAST As an input it gets a single genomic sequence and m RNA FASTA sequences Pseudo genes and paralogues are eliminated in this search and rue gene is selected. 16
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- 18. Nucleotide database- GENEBANK NCBI’sprimary sequence database Comprehensive public database of nucleotide sequences Bibliographic support Built from authors entry into genebak regarding EST Genebank an EMBL make an INSD Collaborative approach to share data daily 18
- 19. HOMOLOGENE Automated detectionof homologues Completely sequenced eukaryotic genes Analyses the proteins of the input organism Blastp Taxonomic trees are being made Statistical analysis of each match is done and orthologs and paralogs are identified 19
- 20. Db SNP Databaseof single nucleotide polymorphisms Short deletion and insertions polymorphisms SNP~ 3D structures via Cn3D and MMDB Functional variants could be matched with the OMIM 20
- 21. Literature database- PMC Pubmed central Digital archive of peer review journals of life sciences Enormous full text journals are there Immediate access to full text journals or within 12 months of publishing 21
- 22. Protein database ENTREZPROTEIN ~ Protein sequence database of NCBI Databases are cross searched PDB, Swiss-Prot Taxonomic relations CDD conserved domain database 22
- 23. Gene expression database Distribution and regulation of the Transcriptional products Normal and abnormal cell types Lot of techniques have been developed for survey of genome wide transcript expression 23
- 24. SAGE map Serialanalysis of gene expression map Gene expression data analysis Tag-to-gene function map SAGE tags to gene clusters or a single gene A reciprocal gene to tag SAGE Map is also available Updated weekly 24
- 25. Structural database- MMDB Molecular modeling database MMDB 3D macromolecular structures XRD and NMR are being used for the experimental structure determination Evolutionary history of function Relationship between macromolecules. 25
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- 30. Chemical database- Pubchem Database for the chemical molecules Freely accessed through web-user interface Chemical structure Diagnostic and therapeutic agents Molecular mass below 2000u Bridge between macromolecular genomics and small organic molecules of cellular metabolism 30
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