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Interactive InterPro-based comparisons of proteins in whole genomes

A. Kanapin, R. Apweiler, M. Biswas, W. Fleischmann, Y. Karavidopoulou, P. Kersey, E. V. Kriventseva, V. Mittard, N. Mulder, T. Oinn, I. Phan, F. Servant (+1 others)
<span title="2002-02-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes  ...  coding sequences of the complete genomes of bacteria, archaea and eukaryotes.  ...  Fig. 1 . 1 The top section of the form used for setting up interactive InterPro-based comparisons of proteins in whole genomes. c Oxford University Press 2002  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/18.2.374">doi:10.1093/bioinformatics/18.2.374</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11847096">pmid:11847096</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zyagz24525eo3nyjimdhw27xw4">fatcat:zyagz24525eo3nyjimdhw27xw4</a> </span>
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Applications of InterPro in protein annotation and genome analysis

M. Biswas
<span title="2002-01-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
InterPro in Proteome Analysis Comparative analyses Interactive InterPro-based proteome comparisons between any of the organisms in the database can be carried out using a web-based tool 11, 15 that  ...  : Interactive InterPro-based proteome comparisons can be carried out using this web-based tool browser. 18 Mapping of InterPro entries to GO terms thus provides an automatic means of assigning GO terms  ... 
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Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes

R. Apweiler
<span title="2001-01-01">2001</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 two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes.  ...  The Proteome Analysis Database is accompanied by a program that has been designed to carry out InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database  ...  Interactive comparisons (dynamic HTML pages) Dynamic InterPro-based comparisons can be made using the InterPro proteome comparisons program to select the proteomes of the organisms to be compared and the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/29.1.44">doi:10.1093/nar/29.1.44</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11125045">pmid:11125045</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC29822/">pmcid:PMC29822</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ug42g6zpf5bsfoam7zavbsvlki">fatcat:ug42g6zpf5bsfoam7zavbsvlki</a> </span>
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Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome

Jingyin Yu, Linhai Wang, Hui Guo, Boshou Liao, Graham King, Xiurong Zhang
<span title="2017-03-24">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Whole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty.  ...  Our comparison-of-function analyses for different classes of gene pairs indicated that the WGD and TD evolutionary events were both responsible for introducing genes that enabled exploration of novel and  ...  Xin Zhou in Washington University in St. Louis and Dr. Komivi Dossa in Oil Crops Research Institute in Chinese Academy of Agricultural Sciences for the critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-3599-4">doi:10.1186/s12864-017-3599-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28340563">pmid:28340563</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5364699/">pmcid:PMC5364699</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/weffjhqq65g6vfn6fvq2jxotz4">fatcat:weffjhqq65g6vfn6fvq2jxotz4</a> </span>
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Clustering and analysis of protein families

Evgenia V Kriventseva, Margaret Biswas, Rolf Apweiler
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
Acknowledgements This work was supported, in part, by grant B104-CT97-2099 from the European Commission.  ...  InterPro is a very useful resource for the computational functional classification of newly determined sequences ( Figure 2 ) and for comparative analysis of whole genomes [14 •• ,15] .  ...  An InterPro-based analysis of the protein family composition and the organisation of protein domains within the proteomes of fly, worm and yeast is also performed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(00)00211-6">doi:10.1016/s0959-440x(00)00211-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11406384">pmid:11406384</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pf4nkex5r5e6npnkdlnysrd6ri">fatcat:pf4nkex5r5e6npnkdlnysrd6ri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811085238/http://dmi.uib.es/~jairo/bio/proteinFamiliesReview.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/14/e1/14e14964ea17381e94efc15b33f9676c74d02dee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(00)00211-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

TEMBLOR – Perspectives of EBI Database Services

Henning Hermjakob, Rolf Apweiler
<span title="">2002</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eaz5kv6drnd7hlqjuszvrhtqnm" style="color: black;">Comparative and Functional Genomics</a> </i> &nbsp;
The availability of complete genomic data allows a whole range of new large-scale experiments such as the generation of whole-genome gene expression data, high-throughput protein identification by mass  ...  Building on the integrated database interface, new tools tools and algorithms will allow the user to perform complex analysis of the data, including whole genome/proteome comparison and complex strutural  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.133">doi:10.1002/cfg.133</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18628871">pmid:18628871</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447230/">pmcid:PMC2447230</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mm66zbhv4rcy5lfi6722twzf54">fatcat:mm66zbhv4rcy5lfi6722twzf54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725071523/http://downloads.hindawi.com/journals/ijg/2002/985406.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/a6/f9/a6f9d320eec75b4267a5cf3e10fc596f3920d666.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.133"> <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/PMC2447230" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum

<span title="2020-01-08">2019</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 identification of orthologs among all PVC genomes allows users to perform large-scale comparative analyses and to identify orthologs of any protein in all genomes integrated in the database.  ...  Phylogenetic relationships of PVC proteins and their closest homologs in RefSeq, comparison of transmembrane domains and Pfam domains, conservation of gene neighborhood and taxonomic profiles can be visualized  ...  ACKNOWLEDGEMENTS We are grateful to Roland Sahli for his support and for providing the computational resources necessary for the development and setup of this database.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz924">doi:10.1093/nar/gkz924</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31665454">pmid:31665454</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145651/">pmcid:PMC7145651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/roux43qtlfav7mzmzknfdidore">fatcat:roux43qtlfav7mzmzknfdidore</a> </span>
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Large Scale Statistical Prediction of Protein-Protein Interaction by Potentially Interacting Domain (PID) Pair

Kyu Kim Wan, Jong Park, Jung Keun Suh
<span title="">2002</span> <i title="Japanese Society for Bioinformatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
We developed a database for the potentially interacting domain pairs (PID) extracted from a dataset of experimentally identified interacting protein pairs (DIP: database of interacting proteins) with InterPro  ...  Protein-protein interaction plays a critical role in biological processes.  ...  J.P was supported partly by IMT2000-C3-4 of Ministry of Information and Communication of Korea. The authors thank Dr. DongHoon Oh for comments and corrections.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11234/gi1990.13.42">doi:10.11234/gi1990.13.42</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/22467prybfdz7jsxevabyltgva">fatcat:22467prybfdz7jsxevabyltgva</a> </span>
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Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

Lorna J Richardson, Neil D Rawlings, Gustavo A Salazar, Alexandre Almeida, David R Haft, Gregory Ducq, Granger G Sutton, Robert D Finn
<span title="2018-10-26">2018</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;
Automatic annotation of protein function is routinely applied to newly sequenced genomes.  ...  While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Peter Karp for help and support with the incorporation of MetaCyc data into Genome Properties. FUNDING  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1013">doi:10.1093/nar/gky1013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30364992">pmid:30364992</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cfganwexh5b5dhq53n2xzypxv4">fatcat:cfganwexh5b5dhq53n2xzypxv4</a> </span>
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Integrating Genomic and Proteomic Data: The Integr8 Project

Manuela Pruess, Paul Kersey, Rolf Apweiler
<span title="2004-12-01">2004</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
High-quality databases from major bioinformatics centres in Europe are included, and some core data and the relationships of biological entities to each other and to entries in other databases are stored  ...  Future developments will especially focus on the Genome Reviews, including mapping not yet annotated protein sequences onto their corresponding genomes, generating new predictions for non-coding RNA genes  ...  Additional comparisons can be customised by the user and generated interactively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2004-9">doi:10.1515/jib-2004-9</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7m7r4o7yj5h4hki3ep2a3yowzy">fatcat:7m7r4o7yj5h4hki3ep2a3yowzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705055654/http://biecoll.ub.uni-bielefeld.de/volltexte/2007/190/pdf/jib-9.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/92/50/9250d21f23207fefac96011493d2611adb4a9857.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2004-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair

Wan Kyu Kim, Jong Park, Jung Keun Suh
<span title="">2002</span> <i title="Universal Academy Press Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf2bmhtlzjh4zjrkh3rivxd2sq" style="color: black;">Genome Informatics Series</a> </i> &nbsp;
We developed a database for the potentially interacting domain pairs (PID) extracted from a dataset of experimentally identified interacting protein pairs (DIP: database of interacting proteins) with InterPro  ...  Protein-protein interaction plays a critical role in biological processes.  ...  These results show that a significant portion of the previously unknown protein interactions can be predicted with high specificity even though a rigorous verification will be necessary in comparison with  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14571373">pmid:14571373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m24q6w3o7jbdzhrye44nzpjxdm">fatcat:m24q6w3o7jbdzhrye44nzpjxdm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812011558/http://www.jsbi.org/pdfs/journal1/GIW02/GIW02F005.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/c2/19/c219c906c1cfa712cd080e0356d29967473796cc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Correlated sequence-signatures as markers of protein-protein interaction

Einat Sprinzak, Hanah Margalit
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
As protein-protein interaction is intrinsic to most cellular processes, the ability to predict which proteins in the cell interact can aid signi®cantly in identifying the function of newly discovered proteins  ...  The proteins in this database have been characterized by their sequence-signatures, as de®ned by the InterPro classi®cation.  ...  The InterPro team is greatly acknowledged for their help.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jmbi.2001.4920">doi:10.1006/jmbi.2001.4920</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11518523">pmid:11518523</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wkxmvif465gmvp3abs5fzhdz2m">fatcat:wkxmvif465gmvp3abs5fzhdz2m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20030314054141/http://www.cs.huji.ac.il:80/~cbsem/Papers/einat_hanah.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/c0/0b/c00bad2af601f25de78183d089785573abc72313.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jmbi.2001.4920"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Mouse Proteome Analysis

A. Kanapin
<span title="2003-06-02">2003</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
The variant-based proteins set (VPS) combines RPS and complete protein sequences representing splice variants not included in RPS.  ...  A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteomes.  ...  , and a Grant-in-Aid for Scientific Research on Priority Areas "Genome Information Science" from the Ministry of Education, Culture, Sports, Science and Technology of Japan to H.M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.978703">doi:10.1101/gr.978703</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12819131">pmid:12819131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC403658/">pmcid:PMC403658</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/26s2qp5ksfcytawtqnyowvvnuu">fatcat:26s2qp5ksfcytawtqnyowvvnuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723020250/https://genome.cshlp.org/content/13/6b/1335.full.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/ef/5d/ef5d125ce9f4512ec1993d0614d1a0026cc426b8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.978703"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403658" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei
<span title="2013-10-27">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;
Novel tools for interactive extraction of protein similarity networks have been added.  ...  SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe.  ...  SIMAP can only be maintained with the help of BOINC and is based on server hardware provided by the University of Vienna.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt970">doi:10.1093/nar/gkt970</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24165881">pmid:24165881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3965014/">pmcid:PMC3965014</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nxbvchfugjd6pa7u7whwbn7idq">fatcat:nxbvchfugjd6pa7u7whwbn7idq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3965014/PMC3965014-gkt970.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/a1/9c/a19ccbdf7fde384a23a0cbf512975b890b23fc1c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt970"> <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/PMC3965014" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A System for Automated Bacterial (genome) Integrated Annotation--SABIA

L. G. P. Almeida, R. Paixao, R. C. Souza, G. C. da Costa, F. J. A. Barrientos, M. T. dos Santos, D. F. de Almeida, A. T. R. Vasconcelos
<span title="2004-04-15">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
A web-based software suite, SABIA (System for Automated Bacterial Integrated Annotation), is described that provides a comprehensive computational support for the assembly and annotation of whole bacterial  ...  genomes from the data derived from sequencing projects.  ...  ACKNOWLEDGEMENTS We thank Andrew Simpson for his help with the final preparation of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth273">doi:10.1093/bioinformatics/bth273</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15087310">pmid:15087310</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ygwek5jty5gl3jvgnklmamzdii">fatcat:ygwek5jty5gl3jvgnklmamzdii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170716201143/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/20/16/10.1093/bioinformatics/bth273/2/bth273.pdf?Expires=1500329504&amp;Signature=FtXDZDd1pItKlJeIDLRHNesHLf2wD-TC-gVWchjyfQdQof~OVHD9VYbTklaZ4ZFLG6-4MR3wK4qSjwOd0laydm8z83si3GbGnIs4yMJ67QJRrND3LK0RAgsA3bzjJOtCqyaJ6phv7W5U6NwO4VPY3H6B-wNGtBAbLgq~~ko-OhNl3lvdIEMhmFiRU1mGdGv-XehkPVbAgvgLv7DoFRHLa1I0dZkvwg~4-2-eAW4-fsDlLz3p2Vu4S6NGLPCTMnwh71MK0w7bR7VFDMhjLVz-lgYPO0JkB4W1J16lltjjk~NK0C7W~~WLm7~JQsnP3j0B6Yq-5VzhO5m6XdhVC1G05Q__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" 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/7e/da/7eda842523e055e6be84f71697e734f853e4ddff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth273"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>
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