BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

被引：698

作者：

van Heel, Auke J. ^{[1
]}

de Jong, Anne ^{[1
]}

Song, Chunxu ^{[1
]}

Viel, Jakob H. ^{[1
]}

Kok, Jan ^{[1
]}

Kuipers, Oscar P. ^{[1
]}

机构：

[1] Univ Groningen, Mol Genet, GBB, NL-9747 AG Groningen, Netherlands

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / W1期

基金：

欧盟地平线“2020”;

关键词：

CHEMICAL-STRUCTURES; PREDICTION; GENES;

D O I：

10.1093/nar/gky383

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Interest in secondary metabolites such as RiPPs (ri-bosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORFcalling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly webinterface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

引用

页码：W278 / W281

页数：4

共 19 条

[1] RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links [J].

Agrawal, Priyesh ;

Khater, Shradha ;

Gupta, Money ;

Sain, Neetu ;

Mohanty, Debasisa .

NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W80-W88

[2] Biosynthesis of the Novel Macrolide Antibiotic Anthracimycin [J].

Alt, Silke ;

Wilkinson, Barrie .

ACS CHEMICAL BIOLOGY, 2015, 10 (11) :2468-2479

[3] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[4] Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature [J].

Arnison, Paul G. ;

Bibb, Mervyn J. ;

Bierbaum, Gabriele ;

Bowers, Albert A. ;

Bugni, Tim S. ;

Bulaj, Grzegorz ;

Camarero, Julio A. ;

Campopiano, Dominic J. ;

Challis, Gregory L. ;

Clardy, Jon ;

Cotter, Paul D. ;

Craik, David J. ;

Dawson, Michael ;

Dittmann, Elke ;

Donadio, Stefano ;

Dorrestein, Pieter C. ;

Entian, Karl-Dieter ;

Fischbach, Michael A. ;

Garavelli, John S. ;

Goeransson, Ulf ;

Gruber, Christian W. ;

Haft, Daniel H. ;

Hemscheidt, Thomas K. ;

Hertweck, Christian ;

Hill, Colin ;

Horswill, Alexander R. ;

Jaspars, Marcel ;

Kelly, Wendy L. ;

Klinman, Judith P. ;

Kuipers, Oscar P. ;

Link, A. James ;

Liu, Wen ;

Marahiel, Mohamed A. ;

Mitchell, Douglas A. ;

Moll, Gert N. ;

Moore, Bradley S. ;

Mueller, Rolf ;

Nair, Satish K. ;

Nes, Ingolf F. ;

Norris, Gillian E. ;

Olivera, Baldomero M. ;

Onaka, Hiroyasu ;

Patchett, Mark L. ;

Piel, Joern ;

Reaney, Martin J. T. ;

Rebuffat, Sylvie ;

Ross, R. Paul ;

Sahl, Hans-Georg ;

Schmidt, Eric W. ;

Selsted, Michael E. .

NATURAL PRODUCT REPORTS, 2013, 30 (01) :108-160

[5] UniProt: the universal protein knowledgebase [J].

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Bye-A-Jee, Hema ;

Cowley, Andrew ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Castro, Leyla Garcia ;

Figueira, Luis ;

Garmiri, Penelope ;

Georghiou, George ;

Gonzalez, Daniel ;

Hatton-Ellis, Emma ;

Li, Weizhong ;

Liu, Wudong ;

Lopez, Rodrigo ;

Luo, Jie ;

Lussi, Yvonne ;

MacDougall, Alistair ;

Nightingale, Andrew ;

Palka, Barbara ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Speretta, Elena ;

Turner, Edward ;

Tyagi, Nidhi ;

Volynkin, Vladimir ;

Wardell, Tony ;

Warner, Kate ;

Watkins, Xavier ;

Zaru, Rossana ;

Zellner, Hermann ;

Xenarios, Ioannis .

NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D158-D169

[6] antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification [J].

Blin, Kai ;

Wolf, Thomas ;

Chevrette, Marc G. ;

Lu, Xiaowen ;

Schwalen, Christopher J. ;

Kautsar, Satria A. ;

Duran, Hernando G. Suarez ;

Santos, Emmanuel L. C. de los ;

Kim, Hyun Uk ;

Nave, Mariana ;

Dickschat, Jeroen S. ;

Mitchell, Douglas A. ;

Shelest, Ekaterina ;

Breitling, Rainer ;

Takano, Eriko ;

Lee, Sang Yup ;

Weber, Tilmann ;

Medema, Marnix H. .

NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W36-W41

[7] Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production [J].

Borrero, Juan ;

Kelly, Eoin ;

O'Connor, Paula M. ;

Kelleher, Philip ;

Scully, Colm ;

Cotter, Paul D. ;

Mahony, Jennifer ;

van Sinderen, Douwe .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2018, 84 (01)

[8] BAGEL: a web-based bacteriocin genome mining tool [J].

de Jong, Anne ;

van Hijum, Sacha A. F. T. ;

Bijlsma, Jetta J. E. ;

Kok, Jan ;

Kuipers, Oscar P. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W273-W279

[9] Identifying bacterial genes and endosymbiont DNA with Glimmer [J].

Delcher, Arthur L. ;

Bratke, Kirsten A. ;

Powers, Edwin C. ;

Salzberg, Steven L. .

BIOINFORMATICS, 2007, 23 (06) :673-679

[10]

Gerst M. M., 2017, GENOME ANNOUNC, V5

← 1 2 →