Colección de bases de datos para la Bioinformática.pdf
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Archivo: Coleccin de bases de datos para la Bioinformtica
Archivo: Bases de datos de DNA
Mdulo
Coleccin de bases de datos para la Bioinformtica
Tcnicas experimentales en Bioqumica
Mdulo II
Tcnicas Experimentales en Bioqumica
Mdulo
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&+
Tcnicas Experimentales en Bioqumica
Mdulo
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+
Tcnicas Experimentales en Bioqumica
Mdulo
*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+
Tcnicas Experimentales en Bioqumica
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