BIOLOGICAL
SEQUENCE
DATABASES
1
NCBI
 What is NCBI?
 National center for biotechnology
information
 Established in 1998
 Part of national library of m...
2 explain Roles of NCBI
1) Maintenance of biological databases
whether primary or secondary. It
includes GENEBANK
2) NCBI ...
Kinds of databases
Primary databases
Secondary
databases
 Original submission by
the experimentalists who
have originally...
NCBI homepage
5
6
NCBI
TOOLS
BLAST
Standard blast Mega blast
PSI-blast PHI-blast
RPS blast
BLAST 2 SEQ
DATABASE
RETREIVAL
TOOL
SPECIALIZED...
Retrieval tool ENTREZ
 Integrated database search and
retrieval system
 Provides extensive links between and
within data...
3 Sequence submission to
NCBI
 Databases are constantly updated
with the newer submissions of the
sequences via sequence ...
Bank it
 Web-based sequence submission tool
 Connect to NCBI Home Page
 Connect to GENEBANK side bar at
left
 Tool of ...
Sequein
 Stand alone sequence submission
and updating tool
 Handling multiple sequence
submission
 Provides increased c...
BLAST
 Basic local alignment search tool
program
 Sequence similarity searches against
a variety of different sequence
d...
Kinds of BLAST
12
Blastn Blastp Blastx Tblastn Tblastx
SPECIALIZED TOOLS
 There are a lot of sequence analysis
tools which will be explained later
1) ORF Finder
2) e-PCR
3) SPI...
ORF FINDER
 Open reading frame finder
 Graphical analysis tool
 Finds all open reading frames in the
user’s sequence or...
e-PCR
 Electronic polymerase chain reaction
 Searches for the STS
 Whole template DNA is searched for
STS
 New databas...
Spidey
 This is another m RNA to genome
alignment tool
 Searches databases via BLAST
 As an input it gets a single geno...
Databases of NCBI
Nucleotide
Literature
Protein
Gene
expression
Structure
Chemical
17
Nucleotide database-
GENEBANK
 NCBI’s primary sequence database
 Comprehensive public database of
nucleotide sequences
...
HOMOLOGENE
 Automated detection of homologues
 Completely sequenced eukaryotic
genes
 Analyses the proteins of the inpu...
Db SNP
 Database of single nucleotide
polymorphisms
 Short deletion and insertions
polymorphisms
 SNP~ 3D structures vi...
Literature database- PMC
 Pubmed central
 Digital archive of peer review journals
of life sciences
 Enormous full text ...
Protein database
 ENTREZ PROTEIN ~ Protein
sequence database of NCBI
 Databases are cross searched
 PDB, Swiss-Prot
 T...
Gene expression database
 Distribution and regulation of the
Transcriptional products
 Normal and abnormal cell types
 ...
SAGE map
 Serial analysis of gene expression
map
 Gene expression data analysis
 Tag-to-gene function map
 SAGE tags t...
Structural database- MMDB
 Molecular modeling database MMDB
 3D macromolecular structures
 XRD and NMR are being used f...
26
27
28
DATABASES
29
Chemical database- Pubchem
 Database for the chemical molecules
 Freely accessed through web-user
interface
 Chemical s...
31
Display settings
32
Aspirin
33
34
Thanks
35
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BIOLOGICAL SEQUENCE DATABASES

  1. 1. BIOLOGICAL SEQUENCE DATABASES 1
  2. 2. NCBI  What is NCBI?  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. 3. 2 explain Roles of 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. 4. Kinds of databases Primary databases 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
  5. 5. NCBI homepage 5
  6. 6. 6 NCBI TOOLS BLAST Standard blast Mega blast 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. 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. 8. 3 Sequence submission to NCBI  Databases are constantly updated with the newer submissions of the sequences via sequence submission tools such as:  Bankit  Sequein 8
  9. 9. Bank it  Web-based sequence 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. 10. Sequein  Stand alone sequence submission and updating tool  Handling multiple sequence submission  Provides increased capacity for long sequence submissions  Multiple annotation  Phylogenetic analysis population 10
  11. 11. BLAST  Basic local alignment search tool program  Sequence similarity searches against a variety of different sequence databases  Unigene, gene, MMDB, GEO 11
  12. 12. Kinds of BLAST 12 Blastn Blastp Blastx Tblastn Tblastx
  13. 13. SPECIALIZED TOOLS  There are a lot of sequence analysis tools which will be explained later 1) ORF Finder 2) e-PCR 3) SPIDEY 13
  14. 14. ORF FINDER  Open reading 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. 15. e-PCR  Electronic polymerase chain reaction  Searches for the STS  Whole template DNA is searched for STS  New database searches a query sequence against a sequence database 15
  16. 16. Spidey  This is another 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
  17. 17. Databases of NCBI Nucleotide Literature Protein Gene expression Structure Chemical 17
  18. 18. Nucleotide database- GENEBANK  NCBI’s primary 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. 19. HOMOLOGENE  Automated detection of 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. 20. Db SNP  Database of 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. 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. 22. Protein database  ENTREZ PROTEIN ~ Protein sequence database of NCBI  Databases are cross searched  PDB, Swiss-Prot  Taxonomic relations  CDD conserved domain database 22
  23. 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. 24. SAGE map  Serial analysis 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. 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
  26. 26. 26
  27. 27. 27
  28. 28. 28
  29. 29. DATABASES 29
  30. 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
  31. 31. 31
  32. 32. Display settings 32
  33. 33. Aspirin 33
  34. 34. 34
  35. 35. Thanks 35
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