ZDB - Comparative genomics database

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)
  
• BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results
  Blanco-M{\'\i}guez, Aitor and Fdez-Riverola, Florentino and S{\'a}nchez, Borja and Louren{\c{c}}o, An{\'a}lia, PLoS One, 13(10):e0205286, 2018 (Pubmed)
  
• CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  Parks, Donovan H and Imelfort, Michael and Skennerton, Connor T and Hugenholtz, Philip and Tyson, Gene W, Genome research, 25(7):1043--1055, 2015 (Pubmed)
  
• Basic local alignment search tool
  Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J, Journal of molecular biology, 215(3):403--410, 1990 (Pubmed)
  
• CDD/SPARCLE: the conserved domain database in 2020
  Lu, Shennan and Wang, Jiyao and Chitsaz, Farideh and Derbyshire, Myra K and Geer, Renata C and Gonzales, Noreen R and Gwadz, Marc and Hurwitz, David I and Marchler, Gabriele H and Song, James S and others, Nucleic acids research, 48(D1):D265--D268, 2020 (Pubmed)
  
• KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold
  Aramaki, Takuya and Blanc-Mathieu, Romain and Endo, Hisashi and Ohkubo, Koichi and Kanehisa, Minoru and Goto, Susumu and Ogata, Hiroyuki, Bioinformatics, 36(7):2251--2252, 2020 (Pubmed)
  
• Sensitive protein alignments at tree-of-life scale using DIAMOND
  Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg, Nature methods, 18(4):366--368, 2021 (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)
  
• 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)
  
• 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)
  
• 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)
  
• 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 NCBI taxonomy database
  Federhen, Scott, Nucleic acids research, 40(D1):D136--D143, 2011 (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)