Published May 21, 2017 | Version v1
Dataset Open

In silico identified signal peptides of Chlamydomonas reinhardtii

Creators

  • 1. University of São Paulo
  • 2. University of California, San Diego

Description

Overview

Chlamydomonas reinhardtii theoretical signal peptides identified by SignalP 4.0 in a protein data set described below:

  • Protein data set came from "The Genome Portal of the Department of Energy Joint Genome Institute" (http://genome.jgi.doe.gov/)
  • Protein sequences were evaluated in SignalP 4.0 Server (http://www.cbs.dtu.dk/services/SignalP/)

 

File used

Chlre4_best_proteins.fasta.gz -> Protein dataset version used for analysis

 

Workflow 

                                          ______Chlre4_best_proteins.fasta.gz_______

                                          |                                                                        |

     Chlre4_best_proteins_fasta_protein_woSP.fasta       Chlre4_best_proteins_signalPeptide.fasta

                                                                                                             |

                                                                      ___Chlre4_best_proteins_signalPeptide_unique.fasta___

                                                                      |                                                                                  |

                                      Chlre4_best_proteins_signalPeptide_unique.aln               Signal Peptide Anotation from aligned.xlsx

 

Info

Chlre4_best_proteins_fasta_protein_woSP.fasta   -> Mature protein sequences from proteins identified without signal peptide

Chlre4_best_proteins_signalPeptide.fasta            -> Identified signal peptide

Chlre4_best_proteins_signalPeptide_unique.fasta -> Unique identified signal peptide

Chlre4_best_proteins_signalPeptide_unique.aln    -> Align signal peptides (UGENE)

Signal Peptide Annotation from aligned.xlsx          -> Signal peptide list, highlighted in orange theoretical tested.

 

Citations

For use of signal peptide dataset, please cite:

Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433

and 

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

doi: 10.1038/nmeth.1701
PMID: 21959131
Supplementary materials: nmeth.1701-S1.pd

and 

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

H. Nordberg, M. Cantor, S. Dusheyko, S. Hua, A. Poliakov, I. Shabalov, T. Smirnova, I. V. Grigoriev, I. Dubchak, ,

Nucleic Acids Res. 42, 26–31. 2014 

doi:10.1093/nar/gkt1069.

 

Files

Files (8.3 MB)

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md5:acc0c7d110dd4412f2d7c9351f5d66ed
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md5:1e196e12e9a679983ecb9918eaa6f1c6
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md5:89f90b5378f9d54259e1b4e2607532ee
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Additional details

References

  • Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12;318(5848):245-50.
  • Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 2014,42(1):D26-31.
  • Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I. The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 2012 Jan;40(Database issue):D26-32.
  • Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods, 8:785-786, 2011