409:
1709:
279:, Ensembl provides researchers a comprehensive resource of relevant biological information about each specific genome. The annotation of the stored reference genomes is automatic and sequence-based. Ensembl encompasses a publicly available genome database which can be accessed via a web browser. The stored data can be interacted with using a graphical UI, which supports the display of data in multiple resolution levels from karyotype, through individual genes, to nucleotide sequence.
1657:
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40:
1669:
259:(HMMs) to derive the final alignment of the sequences. The output of the Clustal Omega may be visualized in a guide tree (the phylogenetic relationship of the best-pairing sequences) or ordered by the mutual sequence similarity between the queries. The main advantage of Clustal Omega over other MSA tools (Muscle,
205:
One of the roles of the EMBL-EBI is to index and maintain biological data in a set of databases, including
Ensembl (housing whole genome sequence data), UniProt (protein sequence and annotation database) and Protein Data Bank (protein and nucleic acid tertiary structure database). A variety of online
337:
The protein entries stored in UniProt are cataloged by a unique UniProt identifier. The annotation data collected for the each entry are organized in logical sections (e.g. protein function, structure, expression, sequence or relevant publications), allowing a coordinated overview about the protein
1027:
Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna; Paramval, Urmila; Pidruchna, Ivanna; Radhakrishnan, Malarvizhi; Tsenkov, Maxim; Nair, Sreenath; Mirdita, Milot; Yeo, Jingi; Kovalevskiy, Oleg; Tunyasuvunakool, Kathryn; Laydon, Agata; Žídek, Augustin; Tomlinson, Hamish; Hariharan, Dhavanthi;
1512:
338:
of interest. Links to external databases and original sources of data are also provided. In addition to standard search by the protein name/identifier, UniProt webpage houses tools for BLAST searching, sequence alignment or searching for proteins containing specific peptides.
325:
is an online repository of protein sequence and annotation data, distributed in UniProt
Knowledgebase (UniProt KB), UniProt Reference Clusters (UniRef) and UniProt Archive (UniParc) databases. Originally conceived as the individual ventures of EMBL-EBI,
236:, GenBank, PIR or EMBL format). Users may also designate the specific databases to be searched, select scoring matrices to be used and other parameters prior to the tool run. The best hits in the BLAST results are ordered according to their calculated
196:
Further, the EMBL-EBI hosts training programs that teach scientists the fundamentals of the work with biological data and promote the plethora of bioinformatic tools available for their research, both EMBL-EBI-based and not so.
282:
Originally centered on vertebrate animals as its main field of interest, since 2009 Ensembl provides annotated data regarding the genomes of plants, fungi, invertebrates, bacteria and other species, in the sister project
1739:
1457:
1749:
1734:
1764:
1421:
1360:
1255:
1439:
354:
AI system freely available to the scientific community. The first release of the database was in 2021; as of 2024, AlphaFold DB provides access to over 214 million protein structures.
221:/RN, and amino acid sequence of proteins, stored in the bioinformatic databases, with the query sequence. The algorithm uses scoring of the available sequences against the query by a
422:
255:(MSA) tool that enables to find an optimal alignment of at least three and maximum of 4000 input DNA and protein sequences. Clustal Omega algorithm employs two profile
1769:
1451:
1774:
1518:
1465:
1366:
363:
1494:
334:(PIR) (housing Protein Sequence Database), the increase in the global protein data generation led to their collaboration in the creation of UniProt in 2002.
206:
services and tools is provided, such as Basic Local
Alignment Search Tool (BLAST) or Clustal Omega sequence alignment tool, enabling further data analysis.
1529:
1754:
1506:
367:
298:(PDB) is a database of three dimensional structures of biological macromolecules, such as proteins and nucleic acids. The data are typically obtained by
1779:
1500:
310:, RCSB, PDBj and BMRB. The database can be accessed through the webpages of its members, including PDBe (housed at the EMBL-EBI). As a member of the
1087:
1789:
432:
303:
1488:
1265:
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121:
1201:
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507:
1523:
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1394:
1377:
392:
382:
327:
229:
62. The highest scoring sequences represent the closest relatives of the query, in terms of functional and evolutionary similarity.
1028:
Abrahamson, Josh; Green, Tim; Jumper, John; Birney, Ewan; Steinegger, Martin; Hassabis, Demis; Velankar, Sameer (5 January 2024).
1325:
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437:
402:
311:
252:
408:
1230:
1030:"AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences"
314:(wwPDB) consortium, PDBe aids in the joint mission of archiving and maintenance of macromolecular structure data.
1673:
1400:
1354:
306:(NMR spectroscopy), and submitted manually by structural biologists worldwide through PDB member organizations –
1383:
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1270:
1123:
1073:
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1331:
1119:
376:
178:
69:
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1225:
578:
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (October 1990). "Basic local alignment search tool".
299:
214:
1596:
190:
217:
is an algorithm for comparing biomacromolecule primary structure, most often nucleotide sequence of
1586:
1513:
International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
1405:
1193:
256:
222:
287:. As of 2020, the various Ensembl project databases together house over 50,000 reference genomes.
271:
Based at the EMBL-EBI, the
Ensembl is a database organized around genomic data, maintained by the
240:(the probability of the presence of a similarly or higher-scoring hit in the database by chance).
1642:
1546:
1349:
603:
780:
Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, et al. (January 2021).
1637:
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984:
885:
811:
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638:
595:
295:
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1389:
1049:
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867:
801:
793:
727:
719:
628:
587:
1308:
347:
284:
1054:
1029:
346:
The AlphaFold
Protein Structure Database (AlphaFold DB) is a collaborative project with
1701:
1096:
979:
954:
880:
855:
806:
781:
732:
707:
633:
276:
174:
1320:
Microsoft
Research - University of Trento Centre for Computational and Systems Biology
591:
1723:
1713:
1571:
1167:
109:
607:
1561:
1556:
1551:
856:"Protein Data Bank: the single global archive for 3D macromolecular structure data"
233:
232:
The database search by BLAST requires input data to be in a correct format (e.g.
97:
39:
1696:
627:. Methods in Molecular Biology. Vol. 395. Humana Press. pp. 149–176.
1632:
1566:
1185:
1147:
622:
427:
263:) is its efficiency, while maintaining a significant accuracy of the results.
553:
656:
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186:
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889:
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741:
642:
797:
599:
1260:
1197:
1189:
1159:
871:
482:
457:
260:
237:
708:"Clustal Omega for making accurate alignments of many protein sequences"
17:
1235:
1181:
1137:
1133:
1129:
1111:
322:
307:
248:
182:
73:
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1002:
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412:
The
European Bioinformatics Institute, Hinxton, Cambridge, UK
1422:
African
Society for Bioinformatics and Computational Biology
1361:
Max Planck
Institute of Molecular Cell Biology and Genetics
755:
275:. Tasked with the continuous annotation of the genomes of
1740:
Buildings and structures in South Cambridgeshire District
1440:
International Nucleotide Sequence Database Collaboration
330:(SIB) (together maintaining Swiss-Prot and TrEMBL) and
142:
955:"UniProt: the universal protein knowledgebase in 2021"
423:
Alternative splicing and transcript diversity database
1685:
458:"Background | European Bioinformatics Institute"
1750:
Information technology organizations based in Europe
1735:
Biological research institutes in the United Kingdom
1765:
Partner institutions of the University of Cambridge
1605:
1539:
1481:
1414:
1301:
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1103:
513:(Press release). EMBL-EBI. 8 April 2024. p. 4.
173:(EMBL) family, focuses on research and services in
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103:
91:
83:
62:
54:
46:
1132:, database of protein sequences grouping together
397:BIG Data Center (National Genomics Data Center),
1367:US National Center for Biotechnology Information
854:Burley, Stephen K.; et al. (January 2019).
1452:International Society for Computational Biology
1519:ISCB Africa ASBCB Conference on Bioinformatics
350:to make predicted protein structures from the
1466:Institute of Genomics and Integrative Biology
1081:
364:National Center for Biotechnology Information
8:
1495:European Conference on Computational Biology
477:
475:
32:
1530:Research in Computational Molecular Biology
953:Bateman, Alex; et al. (January 2021).
1507:International Conference on Bioinformatics
1088:
1074:
1066:
368:United States National Library of Medicine
38:
31:
1501:Intelligent Systems for Molecular Biology
1053:
978:
879:
805:
731:
682:"Clustal Omega Documentation at EMBL-EBI"
632:
1770:Research institutes established in 1992
1692:
1489:Basel Computational Biology Conference
449:
433:European Molecular Biology Organization
304:nuclear magnetic resonance spectroscopy
33:European Bioinformatics Institute (EBI)
1003:"AlphaFold Protein Structure Database"
706:Sievers F, Higgins DG (January 2018).
1775:Research institutes in Cambridgeshire
1446:International Society for Biocuration
1344:European Molecular Biology Laboratory
171:European Molecular Biology Laboratory
122:European Molecular Biology Laboratory
7:
1668:
1472:Japanese Society for Bioinformatics
1434:European Molecular Biology network
358:Other bioinformatics organisations
25:
1755:International research institutes
1524:Pacific Symposium on Biocomputing
1428:Australia Bioinformatics Resource
1395:Swiss Institute of Bioinformatics
1378:Netherlands Bioinformatics Centre
1338:European Bioinformatics Institute
393:Australia Bioinformatics Resource
383:Swiss Institute of Bioinformatics
328:Swiss Institute of Bioinformatics
159:European Bioinformatics Institute
1780:Science and technology in Europe
1707:
1695:
1667:
1656:
1655:
1326:Database Center for Life Science
1314:Computational Biology Department
1202:Arabidopsis Information Resource
1172:Specialised genomic databases:
1790:1992 establishments in England
1373:Japanese Institute of Genetics
373:National Institute of Genetics
167:intergovernmental organization
1:
1293:Rosalind (education platform)
1210:Zebrafish Information Network
1178:Saccharomyces Genome Database
621:Wheeler D, Bhagwat M (2007).
592:10.1016/S0022-2836(05)80360-2
399:Beijing Institute of Genomics
1760:Molecular biology institutes
1730:Bioinformatics organizations
1623:List of biological databases
1142:Protein Information Resource
580:Journal of Molecular Biology
332:Protein Information Resource
169:(IGO) which, as part of the
1116:European Nucleotide Archive
830:"About the Ensembl Project"
657:"Clustal Omega at EMBL-EBI"
438:European Nucleotide Archive
403:Chinese Academy of Sciences
312:Worldwide Protein Data Bank
253:multiple sequence alignment
1806:
1785:Systems science institutes
508:"EMBL-EBI Highlights 2023"
1651:
1401:Wellcome Sanger Institute
1355:J. Craig Venter Institute
37:
1384:Philippine Genome Center
554:"NCBI BLAST at EMBL-EBI"
460:. Ebi.ac.uk. 16 May 2018
1628:Molecular phylogenetics
1124:China National GeneBank
189:, and employs over 600
177:. It is located on the
1332:DNA Data Bank of Japan
1120:DNA Data Bank of Japan
1034:Nucleic Acids Research
959:Nucleic Acids Research
860:Nucleic Acids Research
786:Nucleic Acids Research
413:
377:DNA Data Bank of Japan
201:Bioinformatic services
179:Wellcome Genome Campus
70:Wellcome Genome Campus
1613:Computational biology
1128:Secondary databases:
411:
300:X-ray crystallography
1110:Sequence databases:
1046:10.1093/nar/gkad1011
971:10.1093/nar/gkaa1100
257:Hidden Markov models
191:full-time equivalent
76:, Cambridgeshire, UK
1406:Whitehead Institute
1194:Rat Genome Database
1007:alphafold.ebi.ac.uk
798:10.1093/nar/gkaa942
525:"Scientific report"
117:Parent organization
87:52.079889, 0.186356
34:
27:Centre for research
1643:Sequence alignment
1350:Flatiron Institute
872:10.1093/nar/gky949
756:"Ensembl homepage"
414:
105:Associate Director
1683:
1682:
1638:Sequence database
1152:Protein Data Bank
1146:Other databases:
1040:(D1): D368–D375.
965:(D1): D480–D489.
866:(D1): D520–D528.
792:(D1): D884–D891.
296:Protein Data Bank
155:
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16:(Redirected from
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1618:List of biobanks
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624:BLAST QuickStart
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929:"About UniProt"
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782:"Ensembl 2021"
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1567:Nexus format
1562:NeXML format
1557:FASTQ format
1552:FASTA format
1540:File formats
1337:
1302:Institutions
1037:
1033:
1022:
1010:. Retrieved
1006:
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948:
936:. Retrieved
932:
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911:. Retrieved
907:
904:"About PDBe"
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863:
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837:. Retrieved
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486:
483:"Leadership"
462:. Retrieved
452:
345:
342:AlphaFold DB
336:
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247:
231:
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156:
47:Abbreviation
29:
1547:CRAM format
1468:(CSIR-IGIB)
933:uniprot.org
834:ensembl.org
760:ensembl.org
532:www.embl.de
251:Omega is a
98:Ewan Birney
84:Coordinates
1724:Categories
1633:Sequencing
1597:GTF format
1592:GFF format
1587:VCF format
1577:SAM format
1340:(EMBL-EBI)
1266:SOAP suite
1186:VectorBase
1148:BioNumbers
1134:Swiss-Prot
938:3 November
913:3 November
839:3 November
765:3 November
691:3 November
666:3 November
563:3 November
538:29 October
464:29 October
444:References
428:BioSamples
1460:(ISCB-SC)
1430:(EMBL-AR)
1363:(MPI-CBG)
1104:Databases
1012:22 August
908:ebi.ac.uk
686:ebi.ac.uk
661:ebi.ac.uk
492:21 August
352:AlphaFold
187:Cambridge
55:Formation
1662:Category
1532:(RECOMB)
1482:Meetings
1436:(EMBnet)
1286:Server:
1261:SAMtools
1256:PANGOLIN
1219:Software
1198:PHI-base
1190:WormBase
1160:InterPro
1055:10767828
989:33237286
890:30357364
816:33137190
742:28884485
643:17993672
608:14441902
417:See also
366:(NCBI),
261:ProbCons
225:such as
165:) is an
163:EMBL-EBI
93:Director
63:Location
50:EMBL-EBI
18:EMBL-EBI
1745:Hinxton
1702:Biology
1688:Portals
1674:Commons
1509:(InCoB)
1454:(ISCB)
1442:(INSDC)
1424:(ASBCB)
1328:(DBCLS)
1322:(COSBI)
1236:Clustal
1182:FlyBase
1156:Ensembl
1130:UniProt
1112:GenBank
980:7778908
881:6324056
807:7778975
733:5734385
634:4780883
600:2231712
323:UniProt
318:UniProt
267:Ensembl
249:Clustal
238:E-value
183:Hinxton
138:Website
129:Staff
74:Hinxton
1714:Europe
1515:(CIBB)
1503:(ISMB)
1497:(ECCB)
1474:(JSBi)
1380:(NBIC)
1369:(NCBI)
1357:(JCVI)
1346:(EMBL)
1334:(DDBJ)
1288:ExPASy
1271:TopHat
1251:MUSCLE
1241:EMBOSS
1231:Bowtie
1206:GISAID
1166:, and
1138:TrEMBL
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387:Expasy
385:(SIB:
227:BLOSUM
1526:(PSB)
1448:(ISB)
1397:(SIB)
1386:(PGC)
1316:(CBD)
1280:Other
1246:HMMER
1226:BLAST
604:S2CID
528:(PDF)
511:(PDF)
234:FASTA
215:BLAST
210:BLAST
185:near
1208:and
1174:BOLD
1164:KEGG
1140:and
1122:and
1014:2024
985:PMID
940:2021
915:2021
886:PMID
841:2021
812:PMID
767:2021
738:PMID
693:2021
668:2021
639:PMID
596:PMID
565:2021
540:2019
494:2024
466:2019
308:PDBe
157:The
145:.ebi
58:1992
1050:PMC
1042:doi
975:PMC
967:doi
876:PMC
868:doi
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794:doi
728:PMC
720:doi
629:PMC
588:doi
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302:or
291:PDB
219:DNA
181:in
149:.uk
147:.ac
143:www
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