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HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

T. Lima, A. H. Auchincloss, E. Coudert, G. Keller, K. Michoud, C. Rivoire, V. Bulliard, E. de Castro, C. Lachaize, D. Baratin, I. Phan, L. Bougueleret (+1 others)
<span title="2009-01-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein  ...  Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: www.expasy.org/sprot/hamap).  ...  ACKNOWLEDGEMENTS We wish to thank Alexandre Gattiker for the design and implementation of the initial HAMAP pipeline, Sandrine Pilbout for all the taxonomy-related work, Nicole Redaschi, Thomas Kappler  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn661">doi:10.1093/nar/gkn661</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18849571">pmid:18849571</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2686602/">pmcid:PMC2686602</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/23g5itgmtzflzpvb3mslyv2fgq">fatcat:23g5itgmtzflzpvb3mslyv2fgq</a> </span>
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HAMAP in 2013, new developments in the protein family classification and annotation system

I. Pedruzzi, C. Rivoire, A. H. Auchincloss, E. Coudert, G. Keller, E. de Castro, D. Baratin, B. A. Cuche, L. Bougueleret, S. Poux, N. Redaschi, I. Xenarios (+1 others)
<span title="2012-11-27">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins.  ...  HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap. expasy.org/) is a system for the classification and annotation of protein sequences.  ...  Users may submit individual protein sequences or complete microbial proteomes to be scanned against the entire collection of HAMAP profiles and annotated by HAMAP rules.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks1157">doi:10.1093/nar/gks1157</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23193261">pmid:23193261</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531088/">pmcid:PMC3531088</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sqtfh5uppnhhdoriuglbtrnlsu">fatcat:sqtfh5uppnhhdoriuglbtrnlsu</a> </span>
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Ongoing and future developments at the Universal Protein Resource

<span title="2010-11-04">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Consequently, these entries are in UniProtKB/ Swiss-Prot and manually updated when required. This helps guarantee the high quality of the resulting HAMAP profiles.  ...  UniProt's response was to develop the semi-automated system, HAMAP (high-quality automated and manual annotation of microbial proteomes), that uses manually built annotation templates for protein families  ...  Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1020">doi:10.1093/nar/gkq1020</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21051339">pmid:21051339</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013648/">pmcid:PMC3013648</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vhmcewdzlrfndn3fmtafewqbxa">fatcat:vhmcewdzlrfndn3fmtafewqbxa</a> </span>
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UniProt: a hub for protein information

<span title="2014-10-27">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects.  ...  We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences.  ...  The section of UniProt that contains manually curated and reviewed entries is known as UniProtKB/Swiss-Prot and currently contains about half a million sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku989">doi:10.1093/nar/gku989</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25348405">pmid:25348405</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4384041/">pmcid:PMC4384041</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lypqesbtlbcnhofja5ybswdlhq">fatcat:lypqesbtlbcnhofja5ybswdlhq</a> </span>
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The GOA database in 2009--an integrated Gene Ontology Annotation resource

D. Barrell, E. Dimmer, R. P. Huntley, D. Binns, C. O'Donovan, R. Apweiler
<span title="2009-01-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Over the last five years, the group has augmented the number and coverage of their electronic pipelines and a number of new manual annotation projects and collaborations now further enhance this resource  ...  A range of files facilitate the download of annotations for particular species, and GO term information and associated annotations can also be viewed and downloaded from the newly developed GOA QuickGO  ...  ACKNOWLEDGEMENTS The GOA project would like to thank Serenella Ferro Rojas for her work on mapping UniProtKB/Swiss-Prot Subcellular Locations to GO terms and the GO curators from all collaborating groups  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn803">doi:10.1093/nar/gkn803</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18957448">pmid:18957448</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2686469/">pmcid:PMC2686469</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6rr3sdg375fdharxpzr6xjia6i">fatcat:6rr3sdg375fdharxpzr6xjia6i</a> </span>
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From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase

Ursula Hinz
<span title="2009-12-31">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a5zaemqj4za4nekjggicuat22q" style="color: black;">Cellular and Molecular Life Sciences (CMLS)</a> </i> &nbsp;
With the dramatic increase in the volume of experimental results in every domain of life sciences, assembling pertinent data and combining information from different fields has become a challenge.  ...  In this context, universal knowledgebases play essential roles in providing access to data from complementary types of experiments and serving as hubs with cross-references to many specialized databases  ...  UniProtKB/Swiss-Prot activities at the SIB are supported in addition from the Swiss Federal Government through the Federal Office of Education and Science and from the European Commission contract SLING  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00018-009-0229-6">doi:10.1007/s00018-009-0229-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20043185">pmid:20043185</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2835715/">pmcid:PMC2835715</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yadrwc2stff3fgnukszrfs3hbq">fatcat:yadrwc2stff3fgnukszrfs3hbq</a> </span>
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The Universal Protein Resource (UniProt)

<span title="2007-01-03">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional  ...  The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation.  ...  UniProtKB/Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science, by the European Commission contract FELICS (021902RII3) and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkl929">doi:10.1093/nar/gkl929</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17142230">pmid:17142230</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1669721/">pmcid:PMC1669721</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3doko4bysfhmzddimueyp2tj3y">fatcat:3doko4bysfhmzddimueyp2tj3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218180247/http://pdfs.semanticscholar.org/0f15/d495297f4ed6b03e0c76b35178d2715f5dd5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/15/0f15d495297f4ed6b03e0c76b35178d2715f5dd5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkl929"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669721" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Activities at the Universal Protein Resource (UniProt)

<span title="2013-11-18">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
For example, UniProt has annotated the complete Homo sapiens proteome and 20 000 protein-coding genes are represented by a canonical protein sequence in UniProtKB/Swiss-Prot, with some records describing  ...  UniProtKB/Swiss-Prot currently includes 24 000 curated variants linked to >3000 proteins involved in disease.  ...  Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1140">doi:10.1093/nar/gkt1140</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24253303">pmid:24253303</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3965022/">pmcid:PMC3965022</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ymvqbpyhizafba7upcn222a6ty">fatcat:ymvqbpyhizafba7upcn222a6ty</a> </span>
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Annotation, comparison and databases for hundreds of bacterial genomes

Claudine Médigue, Ivan Moszer
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tyfla3l2drhvfkenf6q5nsaliq" style="color: black;">Research in Microbiology</a> </i> &nbsp;
sites in protein sequences Comparative genomic tools Mauve http://gel.ahabs.wisc.edu/mauve/ Multiple genome alignments in the presence of large-scale evolutionary events MOSAIC Define the set of backbones  ...  This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological  ...  Therefore, two separate sections have been defined: UniProtKB/Swiss-Prot contains manually validated protein entries, and UniProtKB/TrEMBL provides access to computationally annotated records.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.resmic.2007.09.009">doi:10.1016/j.resmic.2007.09.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18031997">pmid:18031997</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bfw4zslyw5bgrdtrxhozk2uc7e">fatcat:bfw4zslyw5bgrdtrxhozk2uc7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809145751/http://www.csub.edu/~kszick_miranda/Medigue%20and%20Moszer%202007.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/bf/d9bfe8b9385f7cfdc2c78df99d1c39040c9a3e7b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.resmic.2007.09.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+45 others)
<span title="2012-05-01">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
InterPro has utility in the large-scale analysis of whole genomes and metagenomes, as well as in characterizing individual protein sequences.  ...  InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based  ...  Integration of the HAMAP database A new member database, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), was added in 2009, InterPro release 22.0.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks456">doi:10.1093/nar/gks456</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3378909/">pmcid:PMC3378909</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oqmafftblfcmdgh4a3i4nzqpzu">fatcat:oqmafftblfcmdgh4a3i4nzqpzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809130739/http://letunic.com/publications/22096229.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ca/7b/ca7bdf24d737de50382ad64be86ada1e43e9cc1a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks456"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378909" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+38 others)
<span title="2011-11-16">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Integration of the HAMAP database A new member database, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), was added in 2009, InterPro release 22.0.  ...  Table 1 . 1 Coverage of the major sequence databases UniProtKB, UniParc and UniMES by InterPro signatures Sequence database Number of proteins in database Number of proteins with one or more matches  ...  Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr948">doi:10.1093/nar/gkr948</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22096229">pmid:22096229</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245097/">pmcid:PMC3245097</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/awtdl7qobjhnveofe7jxno6ju4">fatcat:awtdl7qobjhnveofe7jxno6ju4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108063233/https://hal.inrae.fr/hal-02652188/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/89/c1/89c1fab1d6752729dfa84d989f84973d44c07320.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr948"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245097" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GFam: a platform for automatic annotation of gene families

R. Sasidharan, T. Nepusz, D. Swarbreck, E. Huala, A. Paccanaro
<span title="2012-07-11">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We have developed GFam, a platform for automatic annotation of gene/protein families.  ...  GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from  ...  ACKNOWLEDGEMENTS The authors thank Christopher Wilks for his technical help in integrating the family annotation into the TAIR10 genome release and TAIR curators for providing valuable feedback on the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks631">doi:10.1093/nar/gks631</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22790981">pmid:22790981</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3479161/">pmcid:PMC3479161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g7twtuetgvfdxjyrzcgnrjeiti">fatcat:g7twtuetgvfdxjyrzcgnrjeiti</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3479161/PMC3479161-gks631.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f6/d7/f6d7dfa5534ac6b8f6da6a294360aa226264e256.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks631"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479161" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Solving the Problem: Genome Annotation Standards before the Data Deluge

William Klimke, Claire O'Donovan, Owen White, J. Rodney Brister, Karen Clark, Boris Fedorov, Ilene Mizrachi, Kim D. Pruitt, Tatiana Tatusova
<span title="2011-10-01">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved  ...  NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete  ...  Craig Venter Institute for hosting the workshop and especially Tanja Davidsen and Ramana Madupu for help in the organization before, during, and after the workshop.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.2084864">doi:10.4056/sigs.2084864</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22180819">pmid:22180819</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3236044/">pmcid:PMC3236044</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/57nszc6myncm5grcgonmngldl4">fatcat:57nszc6myncm5grcgonmngldl4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171114030818/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/d6b/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjQwNTYvc2lncy4yMDg0ODY0LnBkZg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/44/66/4466c405e19f5f59fb1fdf0dbc1929686498f4e3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.2084864"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236044" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jose C. Jimenez-Lopez, Emma W. Gachomo, Sweta Sharma, Simeon O. Kotchoni
<span title="">2013</span> <i title="Scientific Research Publishing, Inc,"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ghrh5xzxmvgdxoqq7j42pugmfm" style="color: black;">American Journal of Molecular Biology</a> </i> &nbsp;
of new genes in a wide range of species with fully sequenced genomes.  ...  In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis.  ...  UniProtKB/Swiss-Prot It is a comprehensive, annotated and non-redundant high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/ajmb.2013.32016">doi:10.4236/ajmb.2013.32016</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qqfycymt2fh6pl6ifudliybm2q">fatcat:qqfycymt2fh6pl6ifudliybm2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923103719/http://file.scirp.org/pdf/AJMB_2013043011410133.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/ba/8aba0d34bc010bbe193c4eca431c8d3018ba2882.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/ajmb.2013.32016"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

The European Bioinformatics Institute's data resources

Catherine Brooksbank, Graham Cameron, Janet Thornton
<span title="2009-11-24">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two organisations worldwide providing access to a comprehensive, integrated set of these collections.  ...  Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope with increasing levels of submission, a growing and diversifying user base, and the demand for new types of data.  ...  of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp986">doi:10.1093/nar/gkp986</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19934258">pmid:19934258</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808956/">pmcid:PMC2808956</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lha7vmv3fnhipb7kunhmvunveu">fatcat:lha7vmv3fnhipb7kunhmvunveu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304164926/http://pdfs.semanticscholar.org/c93a/37dcbdc1659fba7dcc73906c14ec9752b9f4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c9/3a/c93a37dcbdc1659fba7dcc73906c14ec9752b9f4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp986"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808956" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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