References & Links

Link to the old AUGUSTUS web server

The old AUGUSTUS web server for predictions with pre-trained models is available at https://bioinf.uni-greifswald.de/augustus/.

References

Please cite the following references when using the AUGUSTUS training web server results in your publication:

Please cite the following references when using results obtained by AUGUSTUS in your publication:

Genome papers, where AUGUSTUS was used in collaboration

  • D. Thybert, M. Roller, F. C. P. Navarro, I. Fiddes, I. Streeter, C. Feig, D. Martin-Galvez, M. Kolmogorov, V. Janoušek, W. Akanni, B. Aken, S. Aldridge, V. Chakrapani, W. Chow, L. Clarke, C. Cummins, A. Doran, M. Dunn, L. Goodstadt, K. Howe, M. Howell, A.-A. Josselin, R. C. Karn, C. M. Laukaitis, L. Jingtao, F. Martin, M. Muffato, S. Nachtweide, M. A. Quail, C. Sisu, M. Stanke, K. Stefflova, C. Van Oosterhout, F. Veyrunes, B. Ward, F. Yang, G. Yazdanifar, A. Zadissa, D. J. Adams, A. Brazma, M. Gerstein, B. Paten, S. Pham, T. M. Keane, D. T. Odom, P. Flicek (2018)
    Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    Genome Research, doi:10.1101/gr.234096.117
  • S. Xu, T. Brockmöller, A. Navarro-Quezada, H. Kuhl, K. Gase, Z. Ling, W. Zhou, C. Kreitzer, M. Stanke, H. Tang, E. Lyons, P. Pandey, S. P. Pandey, B. Timmermann, E. Gaquerel, I. T. Baldwin (2017)
    Wild tobacco genomes reveal the evolution of nicotine biosynthesis
    PNAS, doi:10.1073/pnas.1700073114
  • B. Cai, B. Li, N. Kiga, J. Thusberg, T. Bergquist, Y.-C. Chen, N. Niknafs, H. Carter, C. Tokheim, V. Beleva-Guthrie, C. Douville, R. Bhattacharya, H. T. Grace Yeo, J. Fan, S. Sengupta, D. Kim, M. Cline, T. Turner, M. Diekhans, J. Zaucha, L. R. Pal, C. Cao, C.-H. Yu, Y. Yin, M. Carraro, M. Giollo, C. Ferrari, E. Leonardi, S. C. E. Tosatto, J. Bobe, M. Ball, R. Hoskins, S. Repo, G. Church, S. E. Brenner, J. Moult, J. Gough, M. Stanke, R. Karchin, S. D. Mooney (2017)
    Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges
    Human Mutation. doi:10.1002/humu.23265
  • E. E. Schwager, P. P. Sharma, T. Clarke, D. J. Leite, T. Wierschin, M. Pechmann, Y. Akiyama-Oda, L. Esposito, J. Bechsgaard, T. Bilde, A. D. Buffry, H. Chao, H. Dinh, H. Doddapaneni, S. Dugan, C. Eibner, C. G. Extavour, P. Funch, J. Garb, L. Gonzalez, V. L. Gonzalez, S. Griffiths-Jones, Y. Han, C. Hayashi, M. Hilbrant, D. S. T. Hughes, R. Janssen, S. L. Lee, I. Maeso, S. C. Murali, D. M. Muzny, R. Nunes da Fonseca, C. L. B. Paese, J. Qu, M. Ronshaugen, C. Schomburg, A. Schoenauer, A. Stollewerk, M. Torres-Oliva, N. Turetzek, B. Vanthournout, J. H. Werren, C. Wolff, K. C. Worley, G. Bucher, R. A. Gibbs, J. Coddington, H. Oda, M. Stanke, N. A. Ayoub, N.-M. Prpic, J.-F. Flot, N. Posnien, S. Richards, A. P. McGregor (2017)
    The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
    BMC Biology, 15:62, DOI 10.1186/s12915-017-0399-x
  • K. L. Gendreau, R. A. Haney, E. E. Schwager, T. Wierschin, M. Stanke, S. Richards, J. E. Garb
    House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity (2016)
    BMC Genomics, 18:178, doi:10.1186/s12864-017-3551-7
  • S. König, L. Romoth, L. Gerischer, M. Stanke (2016)
    Simultaneous Gene Finding in Multiple Genomes
    Bioinformatics, 32 (22): 3388-3395, doi: 10.1093/bioinformatics/btw494
  • J. Ulrich, U. Majumdar, C. Schmitt-Engel, J. Schwirz, D. Schultheis, N. Ströhlein, N. Troelenberg, D. Grossmann, T. Richter, J. Dönitz, L. Gerischer, G. Leboulle, A. Vilcinskas, M. Stanke, G. Bucher
    Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target (2015)
    BMC Genomics, https://doi.org/10.1186/s12864-015-1880-y
  • C. Schmitt-Engel, D. Schultheis, J. Schwirz, N. Ströhlein, N. Troelenberg, U. Majumdar, D. Grossmann, T. Richter, M. Tech, J. Dönitz, L. Gerischer, M. Theis, I. Schild, J. Trauner, N.D.B. Koniszewski, E. Köster, S. Kittelmann, Y. Hu, S. Lehmann, J. Siemanowski, J. Ulrich, K.A. Panfilio, R. Schröder, B. Morgenstern, M. Stanke, F. Buchhholz, M. Frasch, S. Roth, E.A. Wimmer, M. Schoppmeier, M. Klingler, G. Bucher (2015)
    The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology
    Nature Communications, doi: 10.1038/ncomms8822
  • B. M. Sadd, S.M. Barribeau, G. Bloch, D. C. de Graaf, P. Dearden, C. G. Elsik, J. Gadau, C. J. P. Grimmelikhuijzen, M. Hasselmann, J. D. Lozier, H. M. Robertson, G. Smagghe, E. Stolle, M. Van Vaerenbergh, R. M. Waterhouse, E. Bornberg-Bauer, S. Klasberg, A. K. Bennett, F. Camara, R. Guigo, K. Hoff, M. Mariotti, M. Munoz-Torres, T. Murphy, D. Santesmasses, G. V. Amdam, M. Beckers, M. Beye, M. Biewer, M. M. G. Bitondi, M. L. Blaxter, A. F. G. Bourke, M. J. F. Brown, S. D. Buechel, R. Cameron, K. Cappelle, J. C. Carolan, O. Christiaens, K. L. Ciborowski, D. F. Clarke, T. J. Colgan, D. H. Collins, A. G. Cridge, T. Dalmay, S. Dreier, L. du Plessis, E. Duncan, S. Erler, J. Evans, T. Falcon, F. C. P. Freitas, T. Fuchikawa, T. Gempe, K. Hartfelder, F. Hauser, S. Helbing, F. C. Humann, F. Irvine, L. S. Jermiin, C. E. Johson, R. M. Johnson, A. K. Jones, T. Kadowaki, J. H. Kidner, V. Koch, A. Köhler, F. B. Kraus, H. M. G. Lattorff, M. Leask, G. A. Lockett, E. B. Mallon, D. S. M. Antonio, M. Marxer, I. Meeus, R. F. A. Moritz, A. Nair, K. Näpflin, I. Nissen, J. Niu, J. G. Oakeshott, A. Osborne, M. Otte, D. G. Pinheiro, N. Rossie, O. Rueppell, C. G. Santos, R. Schmid-Hempel, B. D. Schmitt, C. Schulte, Z. L. P. Simoes, M. P. M. Soares, L. Swevers, E. C. Winnebeck, F. Wolschin, N. Yu, E. M. Zdobnov, P. K. Aqrawi, K. P. Blankenburg, M. Coyle, L. Francisco, A. G. Hernandez, M. Holder, M. E. Hudson, L. Jackson, J. Jayaseelan, V. Joshi, C. Kovar, S. L. Lee, R. Mata, T. Mathew, I. F. Newsham, R. Ngo, G. Okwuonu, C. Pham, L.-L. Pu, N. Saada, J. Santibanez, D. Simmons, R. Thomton, A. Venkat, K. K. O. Walden, Y.-Q. Wu, G. Debyser, B. Devreese, C. Asher, J. Blommaert, A. D. Chipman, L. Chittka, B. Fouks, J. Liu, M. P. O'Neill, S. Sumner, D. Puiu, J. Qu, S. L. Salzberg, S. E. Scherer, D. M. Muzny, S. Richards, G. E. Robinson, R. A. Gibbs, P. Schmid-Hempel, K. C. Worley
    The genomes of two bumblebee species with primitive eusocial organization (2015)
    Genome Biology 16:76, doi:10.1186/s13059-015-0623-3
  • C. G. Elsik, K.C. Worley, A. K. Bennett, M. Beye, F. Camara, C. P. Childers, D.C. Graaf, G. Debyser, J. Deng, B. Devreese, E. Elhaik, J. D. Evans, L. J. Foster, D. Graur, R. Guigo, HGSC production teams, K. J. Hoff, M. E. Holder, M. E. Hudson, G. J. Hunt, H. Jiang, V. Joshi, R. S. Khetani, P. Kosarev, C. L. Kovar, J. Ma, R. Maleszka, R. F. A. Moritz, M. C. Munoz-Torres, T. D. Murphy, D. M. Muzny, I. R. Newsham, J. T. Reese, H. M. Robertson, G. E. Robinson, O. Rueppell, V. Solovyev, M. Stanke, E. Stolle, J. M. Tsuruda, M. Van Vaerenbergh, R. M. Waterhouse, D. B. Weaver, C. W. Whitfield, Y. Wu, E. M. Zdobnov, L. Zhang, D. Zhu, R. A. Gibbs, and on behalf of the Honey Bee Genome Sequencing Consortium (2014)
    Finding the missing honey bee genes: lessons learned from a genome upgrade
    BMC Genomics, doi:10.1186/1471-2164-15-86
  • I.K. Blaby, C.E. Blaby-Haas, N. Tourasse, E.F.Y. Hom, D. Lopez, M. Aksoy, A. Grossman, J. Umen, S. Dutcher, M. Porter, S. King, G.B. Witman, M. Stanke, E.H. Harris, D. Goodstein, J. Grimwood, J. Schmutz, O. Vallon, S.S. Merchant, and S. Prochnik (2014)
    The Chlamydomonas genome project: a decade on
    Trends in Plant Science, 19(10)
  • K. K. Dasmahapatra, J. R. Walters, A. D. Briscoe, J. W. Davey, A. Whibley, N. J. Nadeau, A. V. Zimin, D. S. T. Hughes, L. C. Ferguson, S. H. Martin, C. Salazar, J. J. Lewis, S. Adler, S.-J. Ahn, D. A. Baker, S. W. Baxter, N. L. Chamberlain, R. Chauhan, B. A. Counterman, T. Dalmay, L. E. Gilbert, K. Gordon, D. G. Heckel, H. M. Hines, K. J. Hoff, P. W. H. Holland, E. Jacquin-Joly, F. M. Jiggins, R. T. Jones, D. D. Kapan, P. Kersey, G. Lamas, D. Lawson, D. Mapleson, L. S. Maroja, A. Martin, S. Moxon, W. J. Palmer, R. Papa, A. Papanicolaou, Y. Pauchet, D. A. Ray, N. Rosser, S. L. Salzberg, M. A. Supple, A. Surridge, A. Tenger-Trolander, H. Vogel, P. A. Wilkinson, D. Wilson, J. A. Yorke, F. Yuan, A. L. Balmuth, C. Eland, K. Gharbi, M. Thomson, R. A. Gibbs, Y. Han, J. C. Jayaseelan, C. Kovar, T. Mathew, D. M. Muzny, F. Ongeri, L.-L. Pu, J. Qu, R. L. Thornton, K. C. Worley, Y.-Q. Wu, M. Linares, M. L. Blaxter, R. H. ffrench-Constant, M. Joron, M. R. Kronforst, S. P. Mullen, R. D. Reed, S. E. Scherer, S. Richards, J. Mallet, W. Owen McMillan and C. D. Jiggins (2012)
    Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
    Nature 2012, doi:10.1038/nature11041
  • M. Berriman, B.J. Haas, P.T. LoVerde, R.A. Wilson, G.P. Dillon, G.C. Cerqueira, S.T. Mashiyama, B. Al-Lazikani, L.F. Andrade, P.D. Ashton, M.A. Aslett, D.C. Bartholomeu, G. Blandin, C.R. Caffrey, A. Coghlan, R. Coulson, T.A. Day, A. Delcher, R. DeMarco, A. Djikeng, T. Eyre, J.A. Gamble, E. Ghedin, Y. Gu, C. Hertz-Fowler, H. Hirai, Y. Hirai, R. Houston, A. Ivens, D.A. Johnston, D. Lacerda, C.D. Macedo, P. McVeigh, Z. Ning, G. Oliveira, J.P. Overington, J. Parkhill, M. Pertea, R.J. Pierce, A.V. Protasio, M.A. Quail, M.-A. Rajandream, J. Roger, M. Saji, S.L. Salzberg, M. Stanke, A.R. Tivey, O. Whit, D.L. William, J. Wortman, W. Wu, M. Zamanian, A. Zerlotini, C.M. Fraser-Liggett, B.G. Barrell, N.M. El-Sayed (2009)
    The Genome of the blood fluke Schistosoma mansoni
    Nature 460, 352-358
  • Tribolium Genome Sequencing Consortium,
    The genome of the model beetle and pest Tribolium castaneum.
    Nature, March 2008.
  • Nene, Vishvanath, Wortman, Jennifer R., Lawson, Daniel, Haas, Brian, Kodira, Chinnappa, Tu, Zhijian Jake, Loftus, Brendan, Xi, Zhijong, Megy, Karyn, Grabherr, Manfred, Ren, Quinghu, Zdobnov, Evgeny M., Lobo, Neil F., Campbell, Kathryn S., Brown, Susan E., Bonaldo, Maria F., Zhu, Jingsong, Sinkins, Steven P., Hogenkamp, David G., Amedo, Paulo, Arsenburger, Peter, Atkinson, Peter W., Bidwell, Shelby, Biedler, Jim, Birney, Ewan, Bruggner, Robert V., Costas, Javier, Coy, Monique R., Crabtree, Jonathan, Crawford, Matt, deBruyn, Becky, DeCaprio, David, Eiglmeier, Karin, Eisenstadt, Eric, El-Dorry, Hamza, Gelbart, William M., Gomes, Suely L., Hammond, Martin, Hannick, Linda I., Hogan, James R., Holmes, Michael H., Jaffe, David, Johnston, Spencer J., Kennedy, Ryan C., Koo, Hean, Kravitz, Saul, Kriventseva, Evgenia V., Kulp, David, LaButti, Kurt, Lee, Edward, Li, Song, Lovin, Diane D., Mao, Chunhong, Mauceli, Evan, Menck, Carlos F. M., Miller, Jason R., Montgomery, Philip, Mori, Akio, Nascimento, Ana L., Naveira, Horacio F., Nusbaum, O'Leary, Sinead B., Orvis, Joshua, Pertea, Mihaela, Quesneville, Hadi, Reidenbach, Kyanne R., Rogers, Yu-Hui, Roth, Charles W., Schneider, Jennifer R., Schatz, Michael, Shumway, Martin, Stanke, Mario, Stinson, Eric O., Tubio, Jose M. C., VanZee, Janice P., Verjovski-Almeida, Sergio, Werner, Doreen, White, Owen, Wyder, Stefan, Zeng, Qi, Zhao, Qi, Zhao, Yongmei, Hill, Catherine A., Raikhel, Alexander S., Soares, Marcelo B., Knudson, Dennis L., Lee, Norman H., Galagan, James, Salzberg, Steven L., Paulsen, Ian T., Dimopoulos, George, Collins, Frank H., Bruce, Birren, Fraser-Liggett, Claire M., Severson, David W. (2007)
    Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
    Science, doi: 10.1126/science.1138878
  • Elodie Ghedin, Shiliang Wang, David Spiro, Elisabet Caler, Qi Zhao, Jonathan Crabtree, Jonathan E. Allen, Arthur L. Delcher, David B. Guiliano, Diego Miranda-Saavedra, Samuel V. Angiuoli, Todd Creasy, Paolo Amedeo, Brian Haas, Najib M. El-Sayed, Jennifer R. Wortman, Tamara Feldblyum, Luke Tallon, Michael Schatz, Martin Shumway, Hean Koo, Steven L. Salzberg, Seth Schobel, Mihaela Pertea, Mihai Pop, Owen White, Geoffrey J. Barton, Clotilde K. S. Carlow, Michael J. Crawford, Jennifer Daub, Matthew W. Dimmic, Chris F. Estes, Jeremy M. Foster, Mehul Ganatra, William F. Gregory, Nicholas M. Johnson, Jinming Jin, Richard Komuniecki, Ian Korf, Sanjay Kumar, Sandra Laney, Ben-Wen Li, Wen Li, Tim H. Lindblom, Sara Lustigman, Dong Ma, Claude V. Maina, David M. A. Martin, James P. McCarter, Larry McReynolds, Makedonka Mitreva, Thomas B. Nutman, John Parkinson, Jose M. Peregri-Alvarez, Catherine Poole, Qinghu Ren, Lori Saunders, Ann E. Sluder, Katherine Smith, Mario Stanke, Thomas R. Unnasch, Jenna Ware, Aguan D. Wei, Gary Weil, Deryck J. Williams, Yinhua Zhang, Steven A. Williams, Claire Fraser-Liggett, Barton Slatko, Mark L. Blaxter, and Alan L. Scott (21 September 2007)
    Draft Genome of the Filarial Nematode Parasite Brugia malayi
    Science, 317 (5845), 1756, doi: 10.1126/science.1145406

User contributed species parameters:

  • The training annotation files of the following species are a courtesy of Jason Stajich:
    Aspergillus fumigatus, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Botrytis cinerea, Candida albicans, Candida guilliermondii, Candida tropicalis, Chaetomium globosum, Coccidioides immitis, Coprinus cinereus, Cryptococcus neoformans gattii, Cryptococcus neoformans neoformans, Debaryomyces hansenii, Encephalitozoon cuniculi, Eremothecium gossypii, Fusarium graminearum, Histoplasma capsulatum, Kluyveromyces lactis, Laccaria bicolor, Lodderomyces elongisporus, Magnaporthe grisea, Neurospora crassa, Phanerochaete chrysosporium, Pichia stipitis, Rhizopus oryzae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Ustilago maydis, Yarrowia lipolytica.
  • The training for sealamprey (Petromyzon marinus) was performed by Falk Hildebrand and Shigehiro Kuraku, based on the genome assembly (PMAR3.0) provided by the Genome Sequencing Center at Washington University School of Medicine (WUGSC) in St. Louis.
  • The training for elephant shark (Callorhinchus milii) was performed by Tereza Manousaki and Shigehiro Kuraku, based on the genome assembly (made up of 1.4x whole genome shotgun reads) available at http://esharkgenome.imcb.a-star.edu.sg/resources.html.
  • The training for Pneumocystis jirovecii was performed by Marco Pagni, Philippe Hauser et al as described in Hauser PM, Burdet FX, Cisse OH, Keller L, Taffe P, Sanglard D, Pagni M., Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite Scavenging Amino Acids from Its Host's Lungs. PLoS One. 2010, Dec 20;5(12):e15152. PubMed PMID: 21188143; PubMed Central PMCID: PMC3004796.