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Alejandro Cuevas Villegas, TM; Ph.D(c)
Bioinform!ica
Tecnolog"a M#dica, $niversidad %an!o Toms.
BASES DE DATOS BIOLGICOS
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Que es una base dedatos?
Son colecciones estructuradas deinformacin!
Se com"onen de unidades b#sicasllamadas regis!ros oen!radas.
Cada re$istro se com"one decam"os% &ue contienen datos"rede'nidos relacionados con elre$istro!
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*++, -../Secuencias nucleot0dicas /!/12!3-- 42!214!3++
Secuencias "rot5icas ,.2!32- /!/42!42-
estructuras 4D +!,3. *+!2/.
Interacciones ( com"le6os 1-!431
Cluster 7ni$ene 8umano ,1!34- **3!1*,Genomas com"letos ( ma"as *.!3,. 2!+/39odos diferenciales en ta:onomia 1-!33+ -34!*-*
dbS9; 8umanos 2!4,, *4!*,+!2.*
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1000
1200
1400
1600
1800
2000
Basesde
datosindex
adas
**,.
*-4
.
*44.
*43.
*1*-
+A online Molecular Biolog0Da!a1aseCollec!ion
http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/http://www.oxfordjournals.org/nar/database/cap/ -
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Ten m'or!an! Bioinforma!icsDa!a1ases
GenBan> !ncbi!nlm!ni8!$o@ nucleotide se&uencesEnsembl !ensembl!or$8umanmouse $enome andot8ers
;ub=ed !ncbi!nlm!ni8!$o@ literature references
9< !ncbi!nlm!ni8!$o@ "rotein se&uencesSISS; "rotein domains
O=I= !ncbi!nlm!ni8!$o@ $enetic diseases
EnF(mes !c8em!&mul!ac!u> enF(mes;DB !rcsb!or$"db "rotein structures
EGG !$enome!ad!6" metabolic "at8a(s
Source: Bioinformatics for Dummies
http://www.ncbi.nlm.nih.gov/http://www.ensembl.org/http://www.ncbi.nlm.nih.gov/http://www.ncbi.nlm.nih.gov/http://www.expasy.ch/http://www.ebi.ac.uk/http://www.ncbi.nlm.nih.gov/http://www.chem.qmul.ac.uk/http://www.rcsb.org/pdb/http://www.genome.ad.jp/http://www.genome.ad.jp/http://www.rcsb.org/pdb/http://www.chem.qmul.ac.uk/http://www.ncbi.nlm.nih.gov/http://www.ebi.ac.uk/http://www.expasy.ch/http://www.ncbi.nlm.nih.gov/http://www.ncbi.nlm.nih.gov/http://www.ensembl.org/http://www.ncbi.nlm.nih.gov/ -
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Bases dedatos
;rimariasarc8i@o
Secundarias
corre$idas
GenBan>E=BLDDBH 7ni;rot ;DB =edline ;ub=ed BI9D
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Bases de da!os 'rimarias de secuencias de nucle*!idos
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DDBH
E9A Geneban>9CBI
+%CD
=antienen las mismas re$las "ara el sometimiento de nue@assecuencias!
=antienen lista de "re'6os determinada "ara identi'car lassecuencias de"ositadas!
Se mantienen sincroniFadas% lo &ue "ermite obtener la mismainformacin inde"endiente de la base de datos usada!
http://www.ddbj.nig.ac.jp/sub/prefix.html%23wgshttp://www.ddbj.nig.ac.jp/sub/prefix.html%23wgs -
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ra ona en an
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Deri@ati@e Se&uence Databases
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FEATURES Location/Qualifiers
source 1..2484 /organism=!omo sa"iens
/mol#t$"e=mR%A
/&'#(ref=ta(on)*+,+
/c-romosome=
/ma"="22"2
gene 1..2484
/gene=0L!1
S 22..22*2
/gene=0L!1
/note=-omolog of S. cere3isiae 0S1 5S6issrot Accession
%um'er 142427 S. cere3isiae 0L!1 59en:an; Accession
%um'er U,)4+*8*
/translation=0SF?A9?>RRLET??%R>AA9E?>QRA%A>@E0>E%LA@S
TS>Q?>?@E99L@L>Q>Q%9T9>R@EL>?ERFTTS@LQSFELAS>ST9FR9E
ALAS>S!?A!?T>TT@TA9@ARASS9@L@A@A9%Q9TQ>T?ELF%>A
TRR@AL@%SEE9@>LE??9RS?!%A9>SFS?@@Q9ET?A?RTL%AST?%>RS
Gen;e"t GenBan> CDS translations
>gi|463989|gb|AAC50285.1| DNA mim!"#$ %&'!i% '%("&...
0SF?A9?>RRLET??%R>AA9E?>QRA%A>@E0>E%LA@STS>Q?>?...EL>?ERFTTS@LQSFELAS>ST9FR9EALAS>S!?A!?T>TT@TA...
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&2%&34 DERIVATIVE %&3$&+C& DATABA%&
Curatedtranscripts andproteins
Model transcripts and proteins
Assembled Genomic Regions
Chromosome records Human genome
microbial
organelleftp://ftp.ncbi.nih.go/refse!/re"ease/
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Selected
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enBan5 !o ef%e/
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ef%e/ Bene6!s
Non-redundancy
Updates to reflect current sequencedata andbiology
Datavalidation
Formatconsistency
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Ot8er Deri@ati@e Databases
Expressed Sequences
dbSNP
Structure
Gene
and more
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ENTREZ
FINDING RELEVANT
INFORMATION IN NCBI
DATABASES
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ENTREZ:A DISCOVERYSYSTEM
Gene
Ta:onom(
;ub=edabstracts
9ucleotidese&uences
;roteinse&uences
4DStructur
e
7 8D%!ruc!u
re
!ord 'eight
(AS$
)*AS$)*AS$
Ph+logen+
(ard )in&*eighbors
'e"ated Se!uences*eighbors
'e"ated Se!uences
B)in&+o,ains
*eighbors
'e"ated Structures
Pre-computed and pre-compiled data.
- potentia" go"d ,ine of undiscoered
re"ationships.
0sed "ess than expected.
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(Databases
1he 2ntre3 s4ste,: 58 6and counting7 integrated databases
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Traditional =et8od T8e lin>s menu+*- Se!uence
*uc"eotide rotein )in&
'e"ated roteins
rotein Structure )in&
59+ Structure
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T8e ;roblem
Rapidly growing databases with complex
andchanging relationships
Rapidly changing interfaces to match the
above
Result
Many people dont know:
Where to begin
Where to click on a Web page
Wh it miht be useful to click there
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Global 9CBI EntreF Searc8
colon cancer
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o a n reF earc
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ENTREZ TIP:STARTSEARCHES IN GENE
ther 2ntre3 +Bs
9omoloene
EntreF;rotein
Gene
7niGene
B)in&
(o,o"ogene:
%ene *eighbors
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;recise
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=LJ* Gene
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=LJ*Lin>s to Se&uence
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GE9EMIE J7=A9 =LJ* VARIATIONS
-1ase do,ain
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TAKE HOME MESSAGE ADVANTAGES
OF DATA INTEGRATION
More relevantinter-relatedinformation in oneplace
Makes it easier to find additional relevant
information related to your initial query
Potentially find informationindirectlylinked,butrelevantto your subject of interest
uncovernon-obviousgenetic features that explainphenotype or disease
Easier to build a story based onmultiplepiecesof biological evidence