Chlamydiae Database version 2.0 (June 2019)

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Credits

• High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.
  Pallen, Mark J and Loman, Nicholas J and Penn, Charles W, Current opinion in microbiology, 13(5):625--31, 2010 (Pubmed)
  
• UniProt: the universal protein knowledgebase
  UniProt Consortium and others, Nucleic acids research, 46(5):2699, 2018 (Pubmed)
  
• BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences
  Kanehisa, Minoru and Sato, Yoko and Morishima, Kanae, Journal of molecular biology, 428(4):726--731, 2016 (Pubmed)
  
• KEGG as a reference resource for gene and protein annotation
  Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao, Nucleic acids research, 44(D1):D457--D462, 2015 (Pubmed)
  
• The transporter classification database (TCDB): recent advances
  Saier Jr, Milton H and Reddy, Vamsee S and Tsu, Brian V and Ahmed, Muhammad Saad and Li, Chun and Moreno-Hagelsieb, Gabriel, Nucleic acids research, 44(D1):D372--D379, 2015 (Pubmed)
  
• jvenn: an interactive Venn diagram viewer
  Bardou, Philippe and Mariette, Jérôme and Escudié, Fédéric and Djemiel, Christophe and Klopp, Christophe, BMC bioinformatics, 15(1):293, 2014 (Pubmed)
  
• ETE 3: reconstruction, analysis, and visualization of phylogenomic data
  Huerta-Cepas, Jaime and Serra, François and Bork, Peer, Molecular biology and evolution, 33(6):1635--1638, 2016 (Pubmed)
  
• InterProScan 5: genome-scale protein function classification
  Jones, Philip and Binns, David and Chang, Hsin-Yu and Fraser, Matthew and Li, Weizhong and McAnulla, Craig and McWilliam, Hamish and Maslen, John and Mitchell, Alex and Nuka, Gift and others, Bioinformatics, 30(9):1236--1240, 2014 (Pubmed)
  
• The Pfam protein families database: towards a more sustainable future
  Finn, Robert D and Coggill, Penelope and Eberhardt, Ruth Y and Eddy, Sean R and Mistry, Jaina and Mitchell, Alex L and Potter, Simon C and Punta, Marco and Qureshi, Matloob and Sangrador-Vegas, Amaia and others, Nucleic acids research, 44(D1):D279--D285, 2015 (Pubmed)
  
• Expanded microbial genome coverage and improved protein family annotation in the COG database
  Galperin, Michael Y and Makarova, Kira S and Wolf, Yuri I and Koonin, Eugene V, Nucleic acids research, 43(D1):D261--D269, 2014 (Pubmed)
  
• OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
  Emms, David M and Kelly, Steven, Genome biology, 16(1):157, 2015 (Pubmed)
  
• neXtProt: a knowledge platform for human proteins
  Lane, Lydie and Argoud-Puy, Ghislaine and Britan, Aurore and Cusin, Isabelle and Duek, Paula D and Evalet, Olivier and Gateau, Alain and Gaudet, Pascale and Gleizes, Anne and Masselot, Alexandre and others, Nucleic acids research, 40(D1):D76--D83, 2011 (Pubmed)
  
• Circos: An information aesthetic for comparative genomics
  Krzywinski, Martin and Schein, Jacqueline and Birol, Inanç and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A, Genome Research, 19(9):1639, 2009 (Pubmed)
  
• GenomeDiagram: a python package for the visualization of large-scale genomic data
  Pritchard, Leighton and White, Jennifer A and Birch, Paul RJ and Toth, Ian K, Bioinformatics, 22(5):616--617, 2005 (Pubmed)
  
• RefSeq: an update on prokaryotic genome annotation and curation
  Haft, Daniel H and DiCuccio, Michael and Badretdin, Azat and Brover, Vyacheslav and Chetvernin, Vyacheslav and O’Neill, Kathleen and Li, Wenjun and Chitsaz, Farideh and Derbyshire, Myra K and Gonzales, Noreen R and others, Nucleic acids research, 46(D1):D851--D860, 2017 (Pubmed)
  
• MAFFT multiple sequence alignment software version 7: improvements in performance and usability
  Katoh, Kazutaka and Standley, Daron M, Molecular biology and evolution, 30(4):772--780, 2013 (Pubmed)
  
• FastTree 2--approximately maximum-likelihood trees for large alignments
  Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P, PloS one, 5(3):e9490, 2010 (Pubmed)
  
• The STRING database in 2017: quality-controlled protein--protein association networks, made broadly accessible
  Szklarczyk, Damian and Morris, John H and Cook, Helen and Kuhn, Michael and Wyder, Stefan and Simonovic, Milan and Santos, Alberto and Doncheva, Nadezhda T and Roth, Alexander and Bork, Peer and others, Nucleic Acids Research, 45(Database issue):D362, 2017 (Pubmed)
  
• eggNOG v4.0: nested orthology inference across 3686 organisms
  Powell, Sean and Forslund, Kristoffer and Szklarczyk, Damian and Trachana, Kalliopi and Roth, Alexander and Huerta-Cepas, Jaime and Gabaldon, Toni and Rattei, Thomas and Creevey, Chris and Kuhn, Michael and others, Nucleic acids research, 42(D1):D231--D239, 2014 (Pubmed)
  
• The NCBI taxonomy database
  Federhen, Scott, Nucleic acids research, 40(D1):D136--D143, 2011 (Pubmed)
  
• PaperBLAST: text mining papers for information about homologs
  Price, Morgan N and Arkin, Adam P, MSystems, 2(4):e00039--17, 2017 (Pubmed)
  
• PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
  Yu, Nancy Y and Wagner, James R and Laird, Matthew R and Melli, Gabor and Rey, Sébastien and Lo, Raymond and Dao, Phuong and Sahinalp, S Cenk and Ester, Martin and Foster, Leonard J and others, Bioinformatics, 26(13):1608--1615, 2010 (Pubmed)
  
• DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence
  Xue, Li and Tang, Bin and Chen, Wei and Luo, Jiesi, Bioinformatics, 35(12):2051--2057, 2018 (Pubmed)
  
• Effective—a database of predicted secreted bacterial proteins
  Jehl, Marc-André and Arnold, Roland and Rattei, Thomas, Nucleic acids research, 39(1):D591--D595, 2010 (Pubmed)
  
• High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
  Wang, Yejun and Zhang, Qing and Sun, Ming-an and Guo, Dianjing, Bioinformatics, 27(6):777--784, 2011 (Pubmed)
  
• T3_MM: a Markov model effectively classifies bacterial type III secretion signals
  Wang, Yejun and Sun, Ming'an and Bao, Hongxia and White, Aaron P, PloS one, 8(3):e58173, 2013 (Pubmed)
  
• KEGG Mapper for inferring cellular functions from protein sequences
  Kanehisa, Minoru and Sato, Yoko, Protein Science, -(-):-, 2019 (Pubmed)
  
• Nextflow enables reproducible computational workflows
  Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric, Nature biotechnology, 35(4):316, 2017 (Pubmed)
  
• Snakemake—a scalable bioinformatics workflow engine
  Köster, Johannes and Rahmann, Sven, Bioinformatics, 28(19):2520--2522, 2012 (Pubmed)