ncbi embl notes bioinformatics unit notes

bioinformatics ncbi embl databases

1. Biological
BENJAMIN DISRAELI
7e
more
extensve
a
man's
knowledge
of
what
has
been
done,
the
greater
will
be
his
power
of
knowing
what
to
do.
A. INTRODUCTION
NCBI
(htup://www.ncbi.nlm,nih.gov)
is
a
very
common
name
to
those
who
are
working
in
the
area
of
Bioinformatics
or
Computational
Biology.
It
was
established
in
the
year
1988,
as
a
part
of
the
National
Library
of
Medicine
at
the
National
Institutes
of
Hcalh, Bethesda,
Roles of NCBI
J.
Several
by
researchers
from
all
over
the
Key
features
distinguishing
primary
and
derivative
databases
of
NCBI
Table 4.1
Derivative databases
Primary databases
1.
Built
up
from
primary
data
J.
Origjnal
submission
by
xperimnentalists
2.
Content
controlled
by
third
party
(NCB)
2
Content
controlled
by
the
submitter
Examples:
Refseq
(Reference
Sequence),
RefSNP.
GEO Datasets,
UniGene,
TPA
(Third
Party
Examples: GenBank, SNP Polymorphism), and GEO
(Single Nucleotide
Gene Expression Omnibus)
Sequence Databases
National
Center for
Biotechnology Information
(NCBI)
Maryland,
USA.
Its
aim
was
to
create
public databases,
develop
software
tools
for
sequence
analysis,
and
disseminate
biomedical
information,
mainly
to
aid
the
research
in
computational
biology.
biological
databases
are
maintained
by
NCBI,
noteworthy among them
the nucleic acid
sequence
database,
to
which
data
are
submitted
is GenBank
world.
All
the
databases
of
NCBI are
grouped
into
prinary
and
derivative
databases
(listed
in
Table
4.1);
these
are
elaborated
in
the
later
part
of
the
chapter.
Annotation),
NCBI
Protein,
Structure,
and
Conservation
Domain
Database
(CDD)

2. Biological Sequence Databases
BENJAMIN DIsRAELI
The
more
extensive
a
man's
knowledge
of
what
has
been
done,
the
greater
will
be
his
power
of
knowving
wha
to
do.
A.
National
Center
for
Biotechnology
Information
(NCBI)
INTRODUCTION NCBI
(http://
www.ncbi.nlm.nih.gov)
IS
a
very
common
name
to
those
who
are
working
in
the
area
of
Bioinformatics
or
Computational
Biology.
It
was
established
in
the
year
988,
as
a
part
of
the
National
Library
of
Medicine
at
the
National
Institutes
Roles of NCBI
1.
Several
biological
databases
are
maintained
by
NCBI,
noteworthy among them
by
researchers
from
all
over
the
world.
All
the
databases
of
NCBI
are
grouped
Table
4.1
Key
features
distinguishing
primary
and
derivative
databases
of
NCBI
Derivative databases
Primary databases
1.
Built
up
from
primary
data
I.
Original
submission
by
experimentalists
2.
Content
controlled
by
third
party
(NCBI)
2.
Content
controlled
by
the
submitter
Examples:
Refseq
(Reference
Sequence),
RefSNP,
GEO
Datasets,
UniGene,
TPA
(Third
Party
Annotation),
NCBI
Protein,
Structure,
and
Conservation
Domain
Database
(CDD)
Examples: GenBank, SNP
(Single Nucleotide
Polymorphism), and GEO
(Gene Expression Omnibus)
of
Health,
Bethesda,
Maryland,
USA.
Its
aim
was
to
create
public
databases,
develop
software
tools
for
sequence
analysis,
and
disseminate
biomedical
information,
mainly
to
aid
the
research
in
computational
biology.
the nucleic acid
sequence
database,
to
which
data
are
submitted
is Gen Bank
into
primary
and
derivative
databases
(listed
in
Table
4.l);
these
are
elaborated
in
the
later
part
of
the
chapter.

3. 60
Bioinformatics:
Principles
and
Applications
NCBI
provides
data
retricval
systems
(i.c.,
EntreZz)
3.
It
also
provides
computational
resources
tor
the
analysis
of
a
variety
of
other
biological
data.
GenBarik lata
2
in
TOOLS
AND
DATABASES
OF
NCBI
bio-tools.
Table
4.2
List
of
Brief description
Databases
Scquence
database,
c.g.,
GenBank
Nucleotide
Complete genomes
Genome
Classification
of
organisms
in
NCBI
sequence
datahae
Taxonomy
MMDB
(Molecular
Modelling
Database)
experitnenta
3D structure
2Structure
CDD (Conserved
Domains
Compact
3D
protein
domains
in
MMDB
Online
Mendclian
Inheritance
in
Man
Single Nucleotide Polymorphism
Sequence
Tagged
Site
markers
D Domains
oMIM
R
UniSTS
Data
repository
of
gene
expression
data
Population study datasets
GEO
Do
Gene-based expressed sequence
AUniGene
HomoloGene
ChromOsomal
aberrations
in
cancer
database
Cancer Chromosomes
Gene
cxpression
pattern
in
mouse
CNS
GENSAT
Protein
database
compiled
frorn
various
sourds
Biormedical literature
Protein
M PubMed
Frce
and
full
text
journal
articles
Online text books
YPubMed Central (PMC)
BBooks
tools for We
understanding
and
a
deeper
knowledge
about
these
resources.
These
cat
resources
are
given
in
Fgure
4.1.
NCBI Table
of
42) a
is
storehouse
various
diversificd
databases
(listed
database
resources
available
at
NCBI
Domain Database): Conserved
protein domans
SNP
PopSet
clusters
Eukaryotic homology groups
have
categorized te
all
these
2 resources
of
databases
and

4. Database retrieval
Tool
Lnbica Standard BLAST
MegaBLAST
Entrez
PSI-BLAST
PHI-BLAST
RPS BLAST
BLAST2Sequence
DATABASE RETRIEVAL TOOL
Tools
BLAST
NCBI
Sequence submission
tool (Banklt, Sequin)
ORF finder
e-PCR
Spidey
Biological Sequence Databae,
Specialized tools
Databases
Figure 4.1 Categories of NCBI resources
Nucleotide database
Literature database
Protein database
61
Expression database
Structure database
Chemical database
Other databases
Entrez is an integrated database search and retrieval system that extracts infor
mation from DNA and protein scquence data, population sets, whole genome,
macromolecular structures, and the biomedical literature via PubMed (see Figure
4.2). The sequence sources are different for the database sources, which include Protein
Identification Resource, SWISS-PROT, Protein Data Bank, GenBank protein
translations, and RefSeq. Through PubMed one can access abstracts, references with
links to the full text of the journals available on the web. There are embedded links
leading to NCBI taxonomy. Boolean operators are used for text searching of sequence
or bibliographic records. Further, EntrezZ provides extensive links within and between
database records. In their simplest form, these links may be simple cross-references
between a sequence and the abstract of the paper in which it is reported, or between a
protein sequence and its coding DNA sequence or perhaps its 3D structure. Other
examples are links between a genomic assembly and its components or between a
genomic sequence and those sequences derived from its annotation. Computationally
derived links between 'neighbouring records', such as those based on computed
similarities among sequences or among PubMed abstracts, allow rapid access to groups
of related records. A service called LinkOut expands the range of links to include
external services, from individual database records retated to outside services, including
organism-specific genome databases.
$.G.T.8. Khatsa Coieg

5. 62 Bioinformatics: Prnciples and Applications
Gene
HomoloGene
Genome
Banklt
Sequin
UniGene
Taxonomy
SEQUENCE SUBMISSION TO NCBI
Domains
Figure 4.2
UniSTS
Nucleotide
Entrez
Protein
Structure
SNP
PubMed
Cancer chromosome
(3D domains)
Architecture of the Entrez system
PopSet
GEO
Books
PMC
MeSH
OMIM
The databases are constantly updated through newer submisions of sequences. :
this is done using the following sequence submission tools:
Journals
BankIT is a web-based GenBank sequence submission tool. To use Banklt. it
necessary for the submitters to connect to the NCBI Home Page on the Web at htp
www.ncbi.nlm.nih.gov/ and select the GenBank link from the left sidebar. Bankl:
the tool of choice for simple submissions, especially when only one or a small numte
of records are to be submitted. Banklt can also be used by submitters to update t
existing GenBank records. Sequence analysis tools are not required for submiss.
through this process.
Sequin is a stand-alone software tool developed by NCBI which aids in subms
and updating entries to the sequence databases. It helps in handling multiple sequ
submissions, provides increased capacity for complex submissions conta1niny
sequences.multiple annotations, segmented sets of DNA, or phylogenetic
population studies. Additionally, it provides graphical viewing and editing opt

6. BLAST
Nimilaity cmhen upanst viety ol scquece databascs, euning a l l paped
nlipumets witlh linka full dtaae rods, n Uuene, (iene, the MMIDIS
GO hc detah otalpouttuu ol AS e deall witlh n the Sequeme Alignmenl
Chapte Toconvenre ol undentihy, ll he LASI tool cn be classilied into
|BLAST
blasln
Standard BLAST
Types of hA6L
blastz
ilandard BLAST
Magaf:LAST
MegaBLAST
tal fi lalalas
(Optimized for large bath searhes)
PHIBLA
(Position fpncitc toratnd LAST)
tblastz
PPS BLAST
(Paltsrn Hit Initiats BLAST)
(Rrsverssd Position fpsatr, BLAST)
BLAST26quers
Fiqure 4.3 The overvien of BLAST s availatle at tCeI
As seen in Figure 4.3, standard BLAST includes:
|(Compars two DtIAor protsin sequere)
tdastnJ
1. blastn: comparing the nucleotide vequcn qucry against the nucleotidc
sequence database
2. blastp: comparing the amin0 acid qucry againnt the protein vequens databae
3. blastx: Comparing the nucleotide query equcne translated in all reading
frames ayainst the protcin databae
4. tblastn: comparing the protein qucry cquenc ayainst the nucleotirde dataha
translated in all realing frame,
5. tblastx: comparing siz-TCading frame translations of the nucleotide query
ayainst iz-frame tranation, of the nucleotidc quen databa
MepaBLAST i% a program optinizzd for alipnung long vquenc. McgaBLAST
implerments a greedy alyonthm for tie DNA eyuenus yapped aliznment varch It can
only work with DNA yuene, hene, ths only progran it supports is hlasln For
user onveniene, the MepabLASI pays supports trth Meyas.AST and rcgular
blastn carch.
llercnt catepoeS nhown n pue 4.5

7. ntrins
eghiurng
aralogs or
peogn
STIit not e
ntert n rhe finai
piced
bgnen
The ifferent
pes of
atabuse of
NCBI are
discussed
under the
following major
Cafegne
Nacdende datatuse
Lteratu database
Ptn databasc
Databases of NC8I
Gene greson database
Sectaral atahase
Chemcal databuse
Oher datatases
UCLEOTCE DATABASE
lin ts secton. the prmary sequence database. Gen Bank is elaborated along at
afleremr dvson of sts records and strategy of assigning accession numbers to they
nds s addion to GenBank. many other databases are discussed, such as Ente
ne Entrez gene CnGene. ProtEST. HomoloGene, dbMHC (database for th
Maur Ht-ompatabsty Complex). dbSNP (database of Single Nucleotide Poh
Trg RSen Relerence Sequence). Map Viewer. Evidence Viewer. and Cang
rome
urat entnet (ren Bank is the NCBI's primary sequence database. It s
pee uc talt ase of nucleotide sequences, supporting bibliographc
Ta en Bank makes data available at no cost over the Internet.
imafil Irom the submission of sequence data from authos
Depfevscd sequence tag (EST) (Schuler 1997). gent
and thet high throughput data from the sequenc1ng ce
(bsts . c LMhL Da Library in Europe and the DNA Databuns
Jspa ahlt the lnternational Nucleotide Sequence Databases (INSP
afalerc apptoach lot ckchanging data daily to ensure a uniform
peetcttllcott cquche nformation (see Figure 4.7). Ger Ban Records and
Dvisions
fat (rr. hits cttr iclules a
oncie
descnption of the
sequence.
the
scient ane ad '4tofo o1 "ie sourc
organism,
bibliographic references,
a.C
afca of
hologcal
signiticance. such as
coding regions
and t ts ira. ation5.
Iransciption units. repcat
regions, and sites of
mutatio
and a tabk
ritref weh-based retrieval and analysis services which operalt

8. 70 Bioiformatics, Prinitjes, ard Aplisns
introns. Neiphhouring
paralogs or
pseudogenes
should be in
separate
windows
and
should not be included in the final spliced alignment.
The different types of
datahases of
NCBI are
discussed
under the
following major
categorICs
Nucleotide database
Literature database
Protein database
Gene expression database
Structural databasc
Chemical database
Other databases
Databases of NCBI
NUCLEOTIDE DATABASE
In this section, the primary sequence database, GenBank is elaborated along wit
different division of its records and strategy of assigning accession numbers to thee
records. In addition to GenBank, many other databases are discussed, such as Entre
genome. Entrez gene, UniGene, ProtEST, HomoloGene, dbMHC (database for th:
Major Histo-compatability Complex), dbSNP (database of Single Nucleotide Poly.
morphism). RefSeq (Reference Sequence), Map Viewer, Evidence Viewer, and Cance:
Chromosomes.
GenBank
As already mentioned, GenBank is the NCBI's primary sequence database. It is !
comprehensive public database of nucleotide sequences, supporting bibliographic and
biological annotation. GenBank makes data available at no cost over the Internet,
FTP and a wide range of web-based retrieval and analysis services which operate ot
the Gen Bank data.
GenBank is built primarily from the submission of sequence data from authors a
from the bulk submnission of expressed sequence tag (EST) (Schuler 1997), genol survey sequence (GSS). and other high throughput data from the sequencing cenl GenBank, along with the EMBL Data Library in Europe and the DNA Databans Japan (DDBJ) comprises the International Nucleotide Sequence Databases (N It is a
collaborative approach for exchanging data daily to ensure a unito comprehensive collection of sequence information (see Figure 4.7).
GenBank Records and Divisions
Each Gen Bank entry includes a
concise description of the
sequence, the S
name and taxonomy of the source organism, bibliographic references, and a l
fcatures listing areas of
biological
significance, such as coding regions
and the
protein translations. transcriplion units, repeat regions, and sites of mutat

9. Retrieval
System)
server,
which
is
considercd
as
the
primary
database
retrieva
Database
releases
are
produced
quarterly,
and
integrated
into
the
EBIs
SRS
(Sequ
Figure 4
SEQUENCE RETRIEVAL
Pate
databases Ensembl
automatic
genome
annotation
database.
Structure
Database
(E-MSD),
the
gene
expression
database
available
at
the
EBI
include
the
EMBL
Nucleotide
Sequence
Database,
the
prok
EMBL
is
a
huge
warehouse of
ArrayExpress and t
EMBL ICor
EMBL
and
annotation
with
comprehensive
global
coverage.
(Japan)
and
Gen
Bank
(USA).
This
aims
to
collect
and
present
nucleotide
sequena
International
Nucleotide
Sequence
Database
Collaboration,
which
includes
DDE
and
distributes
nucleotide
sequences
from
the
public
sources.
It
is
a
part
of
te
(EBI)
EMBL (V EMBL (V.
EME
EMBL E#eL
INTRODUCTION
organat
The t
B.
EMBL
Nucleotide
Sequence
Database
also
the
links
to
relevant
records
from
OMIM,
PubMed,
and
Entrez
gene
than
human
and
mouse.The
database
contains
textual
information
and
referen
OMIA
is
a
database
of
genes,
inherited
disorders,
and
traits
in
animal
snent
Online
Mendelian
Inheritance
in
Animals
(OMIA)
GeneTests,
patient
support
groups,
and
many
others.
descriptions,
gene
names,
inheritance
patlerns,
map
locations,
he lle,
databases,
HUGO
(Human
Genome
Organization)
nomenclature
MapView
Entrez
suite
of
databases.
This
is
derived
Irom
the
biomedical
yenes,
gene polymor
orph
distributed
clcetronically
by
the
NCB
(OMIM),
where
it
burgeoning
information
in
human
penctics.
Nraightlorwarl
literature. Eac
Sequence
This was
OMIM
(0Online
Mendelian
Inheritance
in
Man)
knowledye base
surled
by
D
V.
82
Bioinformatics:
Principles
and
Applications
biological
data
and
bio-software.
In
brief,
databas
deposition and data
analysis,
and
make
them
available
to
the
scientific
communt
Swiss
-Prot,
TrEMBL,
UniProt,
and
InterPro,
the
Macromoleculk
prepare biological
databases
and
other
computational
services
to
support
de.
Key
goal
of
the
EMBL
Nucleotide
Sequence
Database
is
to
build,
maintain,
2t
(http://www.ebi.ac.uk),
Hinxton,
Cambridge.
UK.
It
incorporates,
organiz
(http://www.ebi.ac.
uk/emblD)
is
maintained
by
the
Europcan
Bioinformatics
Institu
The
EMBL
(European
Molecular
Biology
Laboratory)
Nucleotide
Sequence
Databa
DNA
and
protein
sequence,
PubMed
references,
general
and
locus-
cilc
mulatwa -Spec
and
detailed
bibliographies,
and
has
numerous
abases
such
lipks
to
other
genetic
dat
entry
has
a
full-text
summary
of
discase
phenotypes
and
includiny
is
inleyaled
will,
Inheritance
in
Man.
McKusick
as
the
detinitive
rcference
Mendelun
the
practice
of
chnical
genetics.
I
is
an
casy
nd
otal
s research
d
nd
genetic
disorders
compiled
to
support
human
genetics
edcate
OMIM
is
a
comprchensive,
authoritative,
nd
timely
ot

10. Figure 4.10
The organizational
Patent Data
EMBL (Contig
EMSL (Contig)
EMBL (WGS updates)
EMBL
(Whole
Genome
Shotgun)
EMBL (WGS release)
EMBL (TPA)
EMBL (Updates)
EMSL
EMBL (Release)
Organization
of
EMBL
database.
The
organization
of
SRS
is
given
in
Figure
4.10.
This
figure
also
porirays
the
7.
EMBLCDS:
Individual
CDS
data
6.
EMBLCON:
Library
containing
CON
entris
$.
EMBLWGS:
Library
containing
WGS
entries.
4.
EMBLTPA:
Librarv
containing
TPA
entries.
ofticial release.
3.
Database. EMBLRELEASE:
The
latest
public
relcase
of
the
EMBL
AucieD
S
e12
Contig. expanded Contig
1.
EMBL:
The
database
in
its
entirety
by
means
of
z
vitual
bb
the following libranes: across
all
available
databanks
can
also
be
eIeuted
l:
SRS.
e
dutz
2re
2v22it
sequence
annotations.
keyWOrds.
and
author
names
Compien
qu
databases
are
searched
with
the
heip
of
SRS
SYstem
sing
2
Dumbe
of
speialized
databanks
along
with
the
main
nucieotide
2nd
prot
The
SRS
server
at
the
EBI
intezrates
and
inks
2
Urehes
2G i
ids icitg
date| T
Sequence
Retrieval
System
(SRS)
via
the
Worid
Wide
Web
here
the
maun
seTce
copses
te
S?S
fowchart of
SRS
Library
of
EMBL
expanded)
EMBLNEW:Library
containing
updated
and
new
enLies
ez1b
sD
t12
i2.
data.
and
patent
dat2
EMBLRELEASE.
EMBLEW.
EMBLTPA.
and
EMBLWGS
Tas
hu
nucleotide
sequence
datz
can
be
2ccessed
viz
emasl
asng
the
t
se
aN
EBIs
FTP
server
prtovides
open
access
to
doanioadabie
datz
bases
d itw2

11. Bioinformatics:
Principles
and
Applications
84
sequence
Sequence Searching
or
Sequence Database can
betwee
is
the
y3.
Compugen's
Bic_SW,
MPsrch,
and
Scanps
are
some
of
the
programs
Tacilitate
more
sensitive
searches
of
protein
sequence
databases.
SEQUENCE
SUBMISSION
AT
EMBL
Submission
of
nucleotide
sequences
is
an
essential
necessity
for
researchers
nure.
computational
analysis.
Moreover,
molecular
biologists
depend
on
free access
databases.
It
has
been
a
regular
practice
for
scientists
to
submt
sequence
informati
to
the
nucleotide
sequence
database
prior
to
publication.
For
permanent
identifcati
of
the
submitted
sequence,
a
unique
accession
number
is
assigned
by
the
database
web-based
interactive
vector
scanning
service
is
available
for
submitters
to
assist
in
screening
of
sequences
tor
vector
contamination
before
submission.
The
vet.
How
to
Submit
Data?
There
are
mainly
three
tools
available
for
submitting
data
at
EMBL.
Irrespective
o
the
tools
adapted
by
the
submitter,
data
confidentiality
is
maintained.
During
t
submission
process
the
submitters
specify
whether
their
Webin
is
an
EMBL
interactive
web-based
system
for
submission
of
nucleoti
sequences
to
the
database.
It
is
designed
to
allow
fast
submission
of
single,
multiple.
very
large
numbers
of
sequences,
Webin
collects
submitter
information,
releases
da:
information,
sequence
data,
description
and
source
information,
reference
citai
information,
and
feature
information
(e.g.,
coding
regions,
regulatory
signals)
reu
to
create
a
database
entry
(shown
in
Figure
4.1l).
Submitters
are
able
to
modily
also
view
their
data
Sequin
is
a
stand-alone
software
tool
(developed
by
the
NCBI)
for
submitng
updating
nucleotide
sequences
to
the
GenBank,
EMBL,
or
DDBJ
databases.
se
contains
a
number
of
bunlt-in
validation
functions
for
enhanced
quality
by are obaita
similarity algorithms prOvided
EBI
A
s
of
set
comprehensive
Irom
EBI
The
can
be
or
website
accessed
interactively
through
email.
by
or
a
as
be
taxoto
searched
whole
individual Nucleotide
F ASTA3 ae
most
commonly used
programs
lor
the
purpose
include The
division.
a
find
will
i
WU-Blast2. FASTA3
single high-scoring
gapped alignment
1s query
nucleotide
sequence
for and proðucit
database
sequences.
astx/y3
used
obtained
between Using the
tlasy
a
protein
sequence
and
translated
DNA
databank
comparisons
between
ComparI
and
a
nucleotide
sequence
protein
databases.
sereening
service
uses
the
latest
implementation
of
the
BLAST
algorithm
and
t.
special
sequence
databank
EMVEC,
compris1ng
a
selection
of
sequences
from
h
SYNthetic
division
of
EMBL
commonly
used
in
the
cloning
and
sequenci
experiments.
submitted
data
can
be
mad
available
to
the
public
immediately
or
whether
the
data
should
be
withheld
until a
author-specified
date.
The
three
tools
of
submission
are
explained
here:
before submission.
assurance
also
a
multiple-platform
software
running
on
Macintosh,
PC/Windows,
and
Computers.

12. Biclcgical Sequence Databases
Secuenca Submitter
Maruscnpt and
aCcession tumber
JOumal
AccesSiCh
TummCer
Faie
Citation update
EMEL Curator
EMBL
heN atabase EMBL elease
Seuerca
sucTisssan
by
Wecin
and
upcate
steos
FGure 411
Seaerca
digrment
sucmissicns
The
submission
of
alignment
data
from
phyloge
Tec
2t
OCzlation
2t2lysis
oÂ
nucieotide
sequences
is
pertormed
by
EMBL's
e
we-oased
system
Webn-Align.
Unique
alignment
numbers
(e.g.
DS32096)
2*
SSei
o
2c1
2gnment
submission
nd
should
be
included
in
the
Eci
s2mssiOn
S
2sstgned
2
uniqe
ccession
number
and
sent
to
the
rSConing
SCiettist
20d
rsearcher
who
submit
the
data.
The
dcvession
follows
a
cla
forma.
Le.
I-5format
(Exampie:
A45621)
and
l-6
format
(Example:
41Iis
ior
zlpabet
and
or
6
is
for
numbers.
Secuerca icentfers
n
aicn
oie
unicue
270
stabie
accessiod
numberS.
EMBL
database
entries
include
Te etce denaters
2nd
versions
hat
specity
changes
in
the
sequences.
The
enoters
hemseives
remam
stabie
wthin
a
gven
entrv.
whereas
the
version
number
crs
wich
every
seuuence
update
Protein
identitiers
can
be
used
by
external
aabses
suca
2
SWISS-PROT
s
denatiers
onto
which
eross-reterences
can
be
ult
2
feature
levei.
e
z..
to
individual
CDS
teatures.
Protein
identifiers
are
currently
2:39127e:i
o
ll
protern
trznslaions
oe
coding
(CDS
features
in
the
nuclevtide
sesuence
22e
enufy
the
dCt
procen
translaon
tor
euch
coding
sequene
hese published
ce
VEXUS.
PHYLIP.
CLUSTAL.
and
GCG
MSF
or
SEQUIN
ASN.I
output
2*
ie
urreniy
zcegtei
standard
ignment
tormats.
EMBL
databaae
preserves
e
innent
ata
rcaived
at
he
EBI
and
it
is
made
available
on
the
EBI's
netvork
ie
auOtly.
proten
aequetce
alignments
are
also
accepted
and
made
272aie
irom
e
EBI
FTP
Server
OEn
enters
can
be
found
in
the
Fearure
Tibie
qualitier
prutein_ú.
lhe
prvtein
u
Tat
or
E\IBL
s
3-3.
i.thre-ietter
pretix
code
tollowed
by
tive
numbes,
tor
amCie
CABcc01
The
ceimal
denotes
version
aumber

13. other databases
scherne
followed
for
such
purpose
facilitates
integration
and
interoperab1lity
organize
FEATURES OF DATABASE
tools
available
at
EBl,
we
have
catalogucd
them
in
Table
4.6
with
essential
explanatv
house
for
various
other
projccts.
To
make
proper
use
of
the
important
sequence
ana
and
motif
identification
using
PPScarch.
There
are
other
applications
developeo
Gene
prediction
using
GeneMark,
pattern
scarching
and
discovery
using
PRA
which
helps
in
performing
multiple
sequence
alignment
and
inference
of
phylogen
EBI
provides
some
specialized
sequence
analysis
programs.
It
includes
CLUSTAL"
dalabases of EN
SEQUENCE ANALYSIS TOOLS
suitable
descriptions
for
the
submissions.
3.
DE
Line
Standards
provide
guidelines
and
database
mitochondrial genome).
2.
EMBL
Annotation
Examples
contain
a
selection
of
EMBL
approved
featur:
table providing
full
cxplanations
of
their
use.
1.
WebFeat
is
a
complete
list
of
feature
table
key
and
qualifier
definitio
EMBL
EBÍ
website
and
from
within
the
Webin.
To
help
the
submitters
annotate
their
sequences,
instructions
are
available
from
th
Procedure for Annotation described. taxonomic
infornation.
This
also
cnsures
that
the
coding
regions
are
corre
submission tools
incorporate
facilities
for
checking
and
providing
additir
entries
to
copc
with
the
BIOLOGICAL
ANNOTATION
AND
DATA
CURATION
with brief descr1ptions. Table 4.
databa,
datahasc,
and
Microarray
datahasc
AIl
these
datahaes
The
sccond
category
of
resoure,
ic.,
tools
or
bio-softwares
The
resources
at
EMBL
can
be
divded
into
1W0
catcgoriss.
namely.
RESOURCES OF EMBL
86
Biiforrnatics
Prrtien
and
kuitatrns
A
popular
databac
management
system
(ORACLE)
is
used
to
data.
conventions for creating
annotations
for
some
common
biological
sequences
(e.g.,
ribosomal
RNA
ovecrwhelming
volurme
of
new
submissions.
For
this
reason
It has
bcen
nccessary
to
automate
many
of
the
steps
involved
in
checking
the
ing translated protein
sequcnce
in
the
protein
databases
TrEMBL
and
SWISS-PD
esscntial
to
provide
locations
of
coding
regions,
to
allow
inclusion
of
the
corres
Scquence
annotation
is
an
essential
part
of
EMBI.
cqucnce
records.
In
particulz.
lools
The
database
includes
Nucleotide
datahae,
Protein
Str
briey are cxplained
in
Table. are listed
4s
daabax