2. *A database is a collection of
information that is organized
so that it can easily be
accessed, managed, and
updated.
*
3. *Harrod’s Librarien’s Glossary
defines, “Database as any grouping
of data for a particular purpose or
for the use of a particular set of end
users, usually organized via fields
and providing tools to enable
manipulation of the data such as
sorting, grouping, extraction and
reporting”.
*
4. Types of Databases
Source database
Reference database
contains references or
contains
citations Informative text, raw data
*
5. Biological
Databses
Biogrid database
Rfam database
Mir base database
Modbase database
6. * The Biological General Repository for
Interaction Datasets (BioGRID) is a curated
biological database of protein-protein and
genetic interactions.
* It wascreated in 2003 by Mike Tyers, Bobby-Joe
Breitkreutz, and Chris Stark at the Samuel
Lunenfeld Research Institute at Mount Sinai
Hospital.
* It strives to provide a comprehensive resource
of protein–protein and genetic interactions for
all major model organism species
*
7.
8. *BiOGRID searches can be performed
by clicking on the “gene” tab from
the main search page.
* To perform search, one can simply
enter term and search engine will
search for matching identifiers.
*Advanced search option can be also
used for the better results.
*
10. * The BioGRID supports wildcard searching (ie.
searching where the search is not exact but
rather a range of possible matches) on the TAIL
end of any keyword entered in our search field.
* To perform a wildcard search, simply enter
your prefix (must be 3 letters or more)
followed by a star (*).
* Examples: STE*, CDC*, YAL01*, CLN*
*
12. *Rfam is an open access
database, hosted at the
Wellcome Trust Sanger
Institute, containing information
about RNA(Ribonucleic acid)
families.
*Rfam contains information for
RNA families and annotations for
millions of RNA genes.
*
15. * To Find Rfam families within your sequence of
interest use Sequence search
* To find multiple sequences to be searched for
matching Rfam families use Batch sequence
* To search for keywords within the textual data in the
Rfam database use Keyword search
* For a complex expression that precisely defines the
species distribution of families use Taxonomy search
* for Search for Rfam families by type like Gene, anti-
toxin etc. use Entry Type search
*
16.
17.
18. * miRBase is a biological database that acts as an
archive of microRNA sequences and
annotations.
* The miRBase registry provides a centralised
system for assigning new names to microRNA
genes.
* The miRBase Sequence database is the primary
repository for published microRNA (miRNA)
sequence and annotation data.
* Database
20. miRBase has five aims:
To provide a consistent naming system for microRNAs
To provide a central place collecting all known microRNA
sequences
To provide human and computer readable information for
each microRNA
To provide primary evidence for each microRNA
To aggregate and link to microRNA target information
21. MiRBase database search features
By miRNA identifier or keyword
By genomic location
For clusters
By tissue expression
By sequence
22. miRBase provides the following services:
The miRBase database is a searchable database of published
miRNA sequences and annotation
Both hairpin and mature sequences are available for searching
and browsing, and entries can also be retrieved by
name, keyword, references and annotation. All sequence and
annotation data are also available for download
Each entry in the miRBase Sequence database represents a predicted
hairpin portion of a miRNA transcript (termed mir in the
database), with information on the location and sequence of the
mature miRNA sequence (termed miR). Both hairpin and mature
sequences are available for searching and browsing, and entries can
also be retrieved by name, keyword, references and annotation.
The miRBase Registry provides miRNA gene hunters with unique
names for novel miRNA genes prior to publication of results.
23. Modbase detabase
MODBASE is a query able database of
annotated protein structure models.
MODBASE contains theoretically calculated
models, which may contain significant
errors, not experimentally determined
structures..
24.
25. Modbase detabase
ModBase Search : ModBase is a database of comparative protein structure models,
calculated by our modeling pipeline ModPipe.
ModBase Search
Search type model (default)
Sequence similarity (blast)
Display type:-
model detail, model overview, sequence overview.
Search by properties.
Database accession number
Annotation keywords
Gene name
26. Advance Search option
Internal id
Template pdb code
Template or homolog pdb code
Organism:-
Homoslapiens
Mas musculus and all
In advance search :-
Select property options:-
Model size, E-value (0-100)
Model score (0-100)
Protein size
% seq. lent (0-100)
Minimum and maximum
Search-(and, or)
Apply to-all models of sequence, some models of a sequence
Hide advanced properties.
27. Modbase provides the following services:
MODBASE uses the MySQL relational database management system for flexible
querying and CHIMERA for viewing the sequences and structures
(http://www.cgl.ucsf.edu/chimera/).
MODBASE is updated regularly to reflect the growth in protein sequence and
structure databases, as well as improvements in the software for calculating
the models.
The largest data set contains 1,26,629 models for domains in 659,495 out of
1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL
database (August 25, 2003); only models based on alignments with significant
similarity scores and models assessed to have the correct fold despite
insignificant alignments are included.
28. The 53 new structures produced by the consortium allowed us to
characterize structurally 24,113 sequences.
Our other resources associated with MODBASE include a comprehensive
database of multiple protein structure alignments
