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BIOLOGICAL
SEQUENCE
DATABASES
1
NCBI
2
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 explain Roles of NCBI
3
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
Kinds of databases
Primary databases
Secondary
4
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.
NCBI homepage
5
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
Retrieval tool ENTREZ
7
Integrated database search and
retrieval system
Provides extensive links between and
within database records
Cross references of different
databases
3 Sequence submission to
NCBI
8
Databases are constantly updated
with the newer submissions of the
sequences via sequence submission
tools such as:
Bankit
Sequein
Bank it
9
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
Sequein
10
Stand alone sequence submission
and updating tool
Handling multiple sequence
submission
Provides increased capacity for long
sequence submissions
Multiple annotation
Phylogenetic analysis population
BLAST
11
Basic local alignment search tool
program
used to generate alignments
between a nucleotide or protein
sequence, referred to as a “query”
and nucleotide or protein sequences
within a database, referred to as
“subject” sequences.
Sequence similarity searches against a
variety of different sequence databases
Unigene, gene, MMDB, GEO
Kinds of BLAST
Blastn Blastp Blastx Tblastn Tblastx
12
SPECIALIZED TOOLS
13
There are a lot of sequence analysis
tools which will be explained later
1) ORF Finder
2) e-PCR
3) SPIDEY
ORF FINDER
14
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
e-PCR
15
Electronic polymerase chain reaction
Searches for the STS (Sequence-
Tagged Sites)
Whole template DNA is searched for
STS
New database searches a query
sequence against a sequence
database
Spidey
16
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.
Databases of NCBI
Nucleotide
17
Literature
Protein
Gene
expression
Structure
Chemical
Nucleotide database-
GENEBANK
18
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
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
Db SNP
20
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
Literature database- PMC
21
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
Protein database
22
ENTREZ PROTEIN ~ Protein
sequence database of NCBI
Databases are cross searched
PDB, Swiss-Prot
Taxonomic relations
CDD conserved domain database
Gene expression database
23
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
SAGE map
24
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
Structural database- MMDB
25
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.
26
27
28
DATABASES
29
Chemical database- Pubchem
30
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
31
Display settings
32
Aspirin
33
34
Thanks
35

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02. Biological sequence databases.pptx

  • 2. NCBI 2 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
  • 3. 2 explain Roles of NCBI 3 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
  • 4. Kinds of databases Primary databases Secondary 4 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.
  • 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. Retrieval tool ENTREZ 7 Integrated database search and retrieval system Provides extensive links between and within database records Cross references of different databases
  • 8. 3 Sequence submission to NCBI 8 Databases are constantly updated with the newer submissions of the sequences via sequence submission tools such as: Bankit Sequein
  • 9. Bank it 9 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
  • 10. Sequein 10 Stand alone sequence submission and updating tool Handling multiple sequence submission Provides increased capacity for long sequence submissions Multiple annotation Phylogenetic analysis population
  • 11. BLAST 11 Basic local alignment search tool program used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences. Sequence similarity searches against a variety of different sequence databases Unigene, gene, MMDB, GEO
  • 12. Kinds of BLAST Blastn Blastp Blastx Tblastn Tblastx 12
  • 13. SPECIALIZED TOOLS 13 There are a lot of sequence analysis tools which will be explained later 1) ORF Finder 2) e-PCR 3) SPIDEY
  • 14. ORF FINDER 14 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
  • 15. e-PCR 15 Electronic polymerase chain reaction Searches for the STS (Sequence- Tagged Sites) Whole template DNA is searched for STS New database searches a query sequence against a sequence database
  • 16. Spidey 16 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.
  • 18. Nucleotide database- GENEBANK 18 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
  • 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. Db SNP 20 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
  • 21. Literature database- PMC 21 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
  • 22. Protein database 22 ENTREZ PROTEIN ~ Protein sequence database of NCBI Databases are cross searched PDB, Swiss-Prot Taxonomic relations CDD conserved domain database
  • 23. Gene expression database 23 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
  • 24. SAGE map 24 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
  • 25. Structural database- MMDB 25 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.
  • 26. 26
  • 27. 27
  • 28. 28
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