all right so we have talked a little bit
about uh the ebi and European databases
and all right similarly we will talk
about another very important database
probably the one that we use more often
in the practicals that is ncbi National
Center of biotechnology information
ncbi when it is formed 1988 basically in
Library of Medicine at the National
Institute of Health okay NIH is involved
with it and uh it it is there to provide
us in its host multiple databases under
this ncbi and that can be sequence
database for Gene sequence database for
proteins and structural database as well
so we will see that what are the aims of
ncbi okay so they can ask you question
from that so what are aims let me let me
talk about the aims okay what are the
names the aim number one is to create
and maintain a public database okay
to create let me write create and
maintain a database second important aim
is uh to provide a retrieval system
retrieval
retrieval system
retrieval system is needed for
retrieving information from the database
a database with so much information will
be of no use if you if you are unable to
retrieve the information so retrieval of
system using what using entries
interest
okay
entries is used in the ncbis to access
information and to retrieve information
from the database okay
and also the third important point is to
develop
software as tools and resources to
analyze
to analyze the data set analyze the
biological data set and also to help in
training
help in
help in computer or computational
biology
compute
stational
biology
training in computational biology to
promote
the database
data deposition and data exchange and
the standard to database data deposition
and exchange all these are aims of
construction of ncbi
okay and the ncbi is what it's a
combination
It's a combination
of databases
combination of DPS okay and what are
such some example of such kind of
database the combination
so let me write it here database this
side and we'll talk about the
description so one of that kind is
nucleotide database
the nucleotide database
in this case this is the sequence
database
DNA sequence RNA sequence database
second type here
genome
genome database is there okay
so where we have complete genome
information
on complete
genome
then third thing
taxonomy databases
taxonomy databases
this is for
classification of an organism so
classification
animal classification plant
classification database
what else we have structural database
sorry structural database
and the example of such kind of
structural database is
molecular modeling database
mmdb molecular modeling database
and we have experimental 3D structure
okay that is the molecular modeling
database where the 3D structure modeling
is prepared and the information is
stored based on the structure of the you
know primary sequence of the protein
we also have domain databases
domain domain of means what proteins
domain okay and one such example is
conserved domain database
conserved domain database CDD
okay there is also 3D domain
molecular modeling domain database mmdd
or mmdb
molecular modeling database
okay and there's one one more kind that
is known as omim
o mean
online mendelian inheritance in men
online
mendelian
inheritance
in men
that is omim omim database
these are all example of databases that
are available
and some more example I'll tell you
SNP
single nucleotide polymorphism database
what else we have
uni STS
that is sequence tag site STS means
sequence tag site
sequence text type markers
okay
then we have unigene
what is unigene
Gene based expressed sequence
then we have
homologene
homolog
what is that homologene
eukaryotic homology group homology group
the database with eukaryotic homology
group
then there is cancer chromosome
databases
where all the chromosomal aberrations
related to cancer is only present
then we have
gen sat
what is genocide all caps
gene expression pattern
in Mouse CNS
where we study gene expression pattern
in the mouse central nervous system
okay
we have Geo database
what about gene expression data
okay
we have pro set
so you can see under ncbi there are even
more databases than under ebi so what
this process is for
population study database
[Music]
okay
and finally the one probably heard
PubMed
PubMed is for biomedical literature and
there is PMC PubMed
Central
which carries free and full text Journal
articles
free
and
full articles
PubMed biomedical literature and PubMed
Central or PNC free full Journal
articles and we have some online
textbooks in books and refseq is a
stable sequence
stable reference sequence for all
molecules corresponding to a central
dogma that is refsec so these are all
the different kinds you know sometimes
they'll ask question related to this you
know one Mass question or two Mass
question that what this particular tool
is useful what this database useful all
you need to understand is that you need
to understand
whether the the term that we are using
whether it's a database
or it's a tool there are difference in
that okay database is a different thing
tool is a different thing
under the database okay for example
these are all databases we're talking
about we're talking about jio we're
talking about gen sat SNP these are all
database where they have the information
regarding the biological system sequence
information structural information uh
and also a storage of information and
access can be done and we can run the
similarity as well but tools are
softwares with which we can access the
database so there is a this difference
okay it's very important to understand
the difference between a database and a
tool a tool is a is something with which
we can gather we can extract
information
we can extract information from database
so for example what is the example of a
tool of ncbi so these are all database
of ncbi right so what is the tool of
ncbi so let me write ncbi tool
and what we'll find out about ncbi tool
enters
so whenever you open this ncbi website
you'll see the enters term
it has a integrated information database
retrieval system so basically it's a DB
retrieval system database retrieval
system
so basically with entrance we can get
information out from any database which
is under ncbi
which has a very simple
user interface with which
all the components of different database
of ncbi are feeded so that we can access
those different information so this is
ncbi
and let's say these are all databases
and this is this user interface where we
have buttons and keys let's say we click
this key then we get information
regarding a DNA
let's say we click this then we have a
sequence of DNA we can run that sequence
match with all the database here and get
the answer so like that okay so this
user interface is enters for ncbi enters
is the biggest
user interface with which we can access
all the databases under
ncbi okay
one more tool that is available so let
me write so ncbi and we're talking about
tools
and remember we have discussed about
enters
enters
now second important tool
most used tool is blast second most used
tool basic local alignment Search tool
blast basic local alignment Search tool
okay
a program for sequence similarity
finding sequence similarity against a
variety of sequence databases so we'll
find
sequence
similarity
against
various
sequence
databases
okay
and there are different kinds of blast
different sorts of blast tools that are
available
let me tell you that okay so the
standard kind of blast what else we have
we have mega blasts
we have what kind of