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Contact info and References

Patrick Douglas edited this page Jul 11, 2018 · 1 revision

Contact Us

User support for Trinotate is provided at the Trinotate Google Group:!forum/trinotate-users

Literature references for software used for functional annotation

  • [Trinity] Full-length transcriptome assembly from RNA-Seq data without a reference genome. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Nature Biotechnology 29, 644�652 (2011)

  • [HMMER] HMMER web server: interactive sequence similarity searching R.D. Finn, J. Clements, S.R. Eddy Nucleic Acids Research (2011) Web Server Issue 39:W29-W37.

  • [PFAM] The Pfam protein families database Punta, P.C. Coggill, R.Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, Ceric, J. Clements, A. Heger, L. Holm, E.L.L. Sonnhammer, S.R. Eddy, A. Bateman, R.D. Finn Nucleic Acids Research (2012) Database Issue 40:D290-D301

  • [SignalP]SignalP 4.0: discriminating signal peptides from transmembrane regions Thomas Nordahl Petersen, Soren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011

  • [tmHMM]Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. J Mol Biol. 2001 Jan 19;305(3):567-80.

  • [BLAST]Basic local alignment search tool. Altschul SF; Gish W; Miller W; Myers EW; Lipman DJ J Mol Biol 215: 403-10 (1990)

  • [KEGG]KEGG for integration and interpretation of large-scale molecular datasets. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; Nucleic Acids Res. 40, D109-D114 (2012).

  • [GO]Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium Nature Genet. 25: 25-29 (2000)

  • [eggNOG]eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16.

  • [RNAMMER] RNammer: consistent annotation of rRNA genes in genomic sequences Lagesen K, Hallin PF, Rodland E, Staerfeldt HH, Rognes T Ussery DW Nucleic Acids Res. 2007 Apr 22.

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