Bases de datos biológicos.pptx

7/21/2019 Bases de datos biolgicos.pptx

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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

Bases de datos biológicos.pptx

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