Colección de bases de datos para la Bioinformática.pdf

8/13/2019 Coleccin de bases de datos para la Bioinformtica.pdf

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Archivo: Bases de datos de DNA

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Coleccin de bases de datos para la Bioinformtica

Tcnicas experimentales en Bioqumica

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Tcnicas Experimentales en Bioqumica

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Bases de datos de DNA

GenBank

GenBank is part of the International Nucleotide Sequence Database ollaboration! "hich comprises

the DN# DataBank of $apan %DDB$&! the European 'olecular Biolo() *aborator) %E'B*&! and

GenBank at NBI+ These three or(ani,ations exchan(e data on a dail) basis+

GenBank%r& is the NI- (enetic sequence database! an annotated collection of all publicl) a.ailable

DN# sequences+ There are approximatel) /0!102!0/3!134 bases in /5!/06!3/0 sequence records in

the traditional GenBank di.isions and 78/!360!163!747 bases in 51!462!583 sequence records in

the 9GS di.ision as of :ebruar) 588/+

E'B*;Bank

The database is produced in an international collaboration"ith GenBank %


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Archivo: Bases de datos de !NA

Archivo: Bases de datos de prote"nas

on a dail) basis+

The E'B* Nucleotide Sequence Database %also kno"n as E'B*;Bank& constitutes Europe=s primar)

nucleotide sequence resource+ 'ain sources for DN# and >N# sequences are direct submissions

from indi.idual researchers! (enome sequencin( pro?ects and patent applications+

DDB$

DDB$ %DN# Data Bank of $apan& is one of the three summit databanks that construct DDB$@E'B*

@GenBank International Nucleotide Sequence Database! throu(h close collaboration "ith EBI inEurope and NBI in N# related topics+

0S ribosomal >N# Database

0S ribosomal >N# is an inte(ral component of the lar(e subunit of all c)toplasmic and most

or(anellar ribosomes+ Its small si,e and association "ith ribosomal as "ell as non;ribosomal

proteins made it an ideal model >N# molecule for studies of >N# structure and >N#;proteininteractions+ The purpose of this database is to pro.ide information on nucleotide sequences of 0S

r>N#s and their (enes+ The sequences for particular or(anisms can be retrie.ed as sin(le files usin(

a taxonomic bro"ser or in multiple sequence structural ali(nments+

Gt>DBA The Genomic t>N# Database

This (enomic t>N# database contains t>N# (ene predictions made b) the pro(ram t>N#scan;SE on

complete or nearl) complete (enomes+ N# databases

# comprehensi.e on;line resource for qualit) checked and ali(ned ribosomal >N# sequence data!

free for academic use+ SI*# pro.ides comprehensi.e! qualit) checked and re(ularl) updated

databases of ali(ned small %73S@7/S! SSN#& sequences for all three domains of life %Bacteria! #rchaea and Eukar)a&+


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Bases de datos de prote"nas

T

The esource %


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En.ironmental Sequences %+

C'D

The Crotein 'utant Database %C'D& co.ers natural as "ell as artificial mutants! includin( random

and site;directed ones! for all proteins except members of the (lobin and immuno(lobulin families+

The C'D is based on literature! not on proteins+ That is! each entr) in the database corresponds to

one article "hich ma) describe one! se.eral or a number of protein mutants+

InterCro

InterCro is a database of protein families! domains! re(ions! repeats and sites in "hich identifiable

features found in kno"n proteins can be applied to ne" protein sequences+ InterCro 72+8 is released

and co.ers 13+5 of ! Gene6D and

S:#'I*H+

DD

DD is a protein annotation resource that consists of a collection of "ell;annotated multiple

sequence ali(nment models for ancient domains and full;len(th proteins+ These are a.ailable as

position;specific score matrices %CSS's& for fast identification of conser.ed domains in protein

sequences .ia >CS;B*#ST+ DD contentincludes NBI;curated domains! "hich use 6D;structure

information to explicitl) to define domain boundaries and pro.ide insi(hts into sequence@structure@function relationships! as "ell as domain models imported from a number of external source

databases%Cfam! S'#>T! G! C>! TIG>:#'&+

Cfam

Cfam is a lar(e collection of multiple sequence ali(nments and hidden 'arko. models co.erin(

man) common protein domains+ Cfam contains ali(nments and models for more than 4888 protein

families! based on the S"issprot and SC;TrE'B* protein sequence databases+

S'#>T

S'#>T %a Simple 'odular #rchitecture >esearch Tool& allo"s the identification and annotation of

(eneticall) mobile domains and the anal)sis of domain architectures+ 'ore than 088 domain

families found in si(nallin(! extracellular and chromatin;associated proteins are detectable+ These

domains are extensi.el) annotated "ith respect to ph)letic distributions! functional class! tertiar)

structures and functionall) important residues+ Each domain found in a non;redundant protein

database as "ell as search parameters and taxonomic information are stored in a relational

eccin de bases de datos para la Bioinformtica http://ev2.us.es/webct/urw/lc396800719041.tp515869535021/selectIt...

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Archivo: Bases de datos de en$imas % rutas metablicas

Archivo: &rincipales bases de datos de or'anismos % ta(onom"a

database s)stem+ END#

B>END# is the main collection of en,)me functional data a.ailable to the scientific communit)+ The

en,)mes are classified accordin( to the En,)me ommission list of en,)mes+ Some 4888 different

en,)mes are co.ered+

E'C;En,)mes and metabolic path"a)s

The E'C Cro?ect! Inc+ "as incorporated in 7222 to pro.ide or(ani,ational! le(al! and financial

support for the E'C (roup pro?ects! such as En,)mes and 'etabolic Cath"a)s Database %E'C& and

'etabolic Cath"a)s Database %'C9&+ E'C@'C9 is the most comprehensi.e sin(le source of

computeri,ed biochemical data a.ailable toda)+ 'oreo.er! this is a po"erful tool for metabolic

reconstruction and modelin(! unmatched in either academia or the (enomics industr)+ Both

databases are currentl) used in a number of public and commercial (enomics pro?ects+

EGGA )oto Enc)clopedia of Genes and Genomes

# (rand challen(e in the post;(enomic era is a complete computer representation of the cell! the

or(anism! and the biosphere! "hich "ill enable computational prediction of hi(her;le.el complexit)of cellular processes and or(anism beha.iors from (enomic and molecular information+ To"ards this

end "e ha.e been de.elopin( a bioinformatics resource named EGG as part of the research

pro?ects of the anehisa *aboratories in the Bioinformatics enter of )oto


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Archivo: )erramientas de anlisis

The 'ICS omprehensi.e Heast Genome Database %HGD& aims to present information on the

molecular structure and functional net"ork of the entirel) sequenced! "ell;studied model

eukar)ote! the buddin( )east Saccharom)ces cere.isiae+ In addition the data of .arious pro?ects on

related )easts are used for comparati.e anal)sis+

SCDA The Cromoter Database of Saccharom)ces cere.isiae

In order to facilitate a s)stematic stud) of the promoters and transcriptionall) re(ulator)

cis;elements of the )east Saccharom)ces cere.isiae on a (enomic scale! "e ha.e de.eloped a

comprehensi.e )east;specific promoter database! SCD+ urrentl) SCD contains 0/8experimentall) mapped transcription factor %T:& bindin( sites and 450 transcriptional start sites

%TSS& as its primar) data entries+ It also contains rele.ant bindin( affinit) and expression data

"here a.ailable+ In addition to mechanisms for promoter information %includin( sequence& retrie.al

and a data submission form! SCD also pro.ides some simple but useful tools for promoter

sequence anal)sis+

ITdB

The


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Archivo: Bases de datos de patentes

This is the ExC#S) %Expert Crotein #nal)sis S)stem& proteomics ser.er of the S"iss Institute of

Bioinformatics %SIB&+ This ser.er is dedicated to the anal)sis of protein sequences and structures as

"ell as 5;D C#GE+

B*#ST

The B*#ST %Basic *ocal #li(nment Search Tool& finds re(ions of local similarit) bet"een sequences+

The pro(ram compares nucleotide or protein sequences to sequence databases and calculates the

statistical si(nificance of matches+ B*#ST can be used to infer functional and e.olutionar)

relationships bet"een sequences as "ell as help identif) members of (ene families+

lustal95

lustal95 is a (eneral purpose multiple sequence ali(nment pro(ram for DN# or proteins+ It

produces biolo(icall) meanin(ful multiple sequence ali(nments of di.er(ent sequences+ It calculates

the best match for the selected sequences! and lines them up so that the identities! similarities and

differences can be seen+ E.olutionar) relationships can be seen .ia .ie"in( lado(rams or

Ch)lo(rams

Ch)lo(en)+fr >obust Ch)lo(enetic #nal)sis :or The Non;Specialist

Ch)lo(en)+fr is a free! simple to use "eb ser.ice dedicated to reconstructin( and anal)sin(

ph)lo(enetic relationships bet"een molecular sequences+ Ch)lo(en)+fr runs and connects .ariousbioinformatics pro(rams to reconstruct a robust ph)lo(enetic tree from a set of sequences+

CDBsum

CDBsum pro.ides an at;a;(lance o.er.ie" of e.er) macromolecular structure deposited in the

Crotein Data Bank %CDB&! (i.in( schematic dia(rams of the molecules in each structure and of the

interactions bet"een them+

odon


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Archivo: *itios de b+s,ueda de protocolos

intellectual propert) protection and facilitates the de.elopment and sharin( of ne" technolo(ies

"orld"ide+

$apanese Catent ffice %$C&

The aim of industrial propert) %IC& s)stem %(eneral term for patent! utilit) model! desi(n! and

trademark s)stems& is to contribute to the nation=s industrial de.elopment throu(h adequate

protection and effecti.e utili,ation of in.entions and other forms of intellectual creations+ To help

promote science and technolo()! the IC s)stem is expected to pla) an increasin(l) important role in

$apan in the 57st centur)+ The $apan Catent ffice %$C& consists of the General #ffairs Department!the Examination Department! the #ppeals Department! and other sections and departments+ The

main functions of these departments includeK 7& (rantin( adequate ri(hts for patents! etc+! 5&

draftin( plans for IC policies! 6& international exchan(e and cooperation! 4& re.ie" of the IC s)stem!

and 0& dissemination of information on IC+ These functions pro.ide for the positi.e ad.ancement of

industrial de.elopment+


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*itios de b+s,ueda de protocolos

BiotechniquesA 'olecular Biolo() Techniques :orum

9elcome to the BioTechniques%r& 'olecular Biolo() :orums! a science;based bulletin board for

techniques! tips! and questions concernin( molecular biolo()! cell biolo()! microscop)! and

bioinformatics

urrent Crotocols

urrent Crotocols is the lar(est collection of authoritati.e and re(ularl);updated step;b);step

research techniques and procedures a.ailable+ 9ith o.er 58 )ears of experience and o.er 77!088

protocols! as "ell as expert Editorial Boards and a qualified in;house scientific editorial staff! urrentCrotocols is the leadin( source of hi(h;qualit) protocols for life scientists "orld"ide+

Crotocol nlineA Hour lab=s referente book

Database of research protocols in bioscience includin( molecular biolo()! cell biolo()! immunolo()!

plant biolo()! de.elopmental biolo()! neuroscience+

>EB#SE

The >estriction En,)me Database is a collection of information about restriction en,)mes and

related proteins+ It contains references! reco(nition and clea.a(e sites! isoschi,omers! commercial

a.ailabilit)! meth)lation sensiti.it)! cr)stal and sequence data+ DN# meth)ltransferases! homin(

endonucleases! nickin( en,)mes! specificit) subunits and control proteins are also included+ 'ostrecentl)! putati.e DN# meth)ltransferases and restriction en,)mes are also listed+


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Colección de bases de datos para la Bioinformática.pdf

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