Amino Acids

, Volume 46, Issue 2, pp 471–473 | Cite as

SECRETOOL: integrated secretome analysis tool for fungi

  • Ana R. Cortázar
  • Ana M. Aransay
  • Manuel Alfaro
  • José A. Oguiza
  • José L. Lavín
Short Communication

Abstract

The secretome (full set of secreted proteins) has been studied in multiple fungal genomes to elucidate the potential role of those protein collections involved in a number of metabolic processes from host infection to wood degradation. Being aminoacid composition a key factor to recognize secretory proteins, SECRETOOL comprises a group of web tools that enable secretome predictions out of aminoacid sequence files, up to complete fungal proteomes, in one step. SECRETOOL is freely available on the web at http://genomics.cicbiogune.es/SECRETOOL/Secretool.php.

Keywords

Protein secretion Signal peptide Secretome Bioinformatics Analysis pipeline 

Supplementary material

726_2013_1649_MOESM1_ESM.pdf (56 kb)
Supplementary material 1 (PDF 56 kb)

References

  1. Bendtsen JD, Jensen LJ, Blom N, von Heijne G, Brunak S (2004) Feature based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel 17(4):349–356PubMedCrossRefGoogle Scholar
  2. Brown NA, Antoniw J, Hammond-Kosack KE (2012) The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis. PLoS One 7(4):e33731. doi:10.1371/journal.pone.0033731 PubMedCentralPubMedCrossRefGoogle Scholar
  3. Caccia D, Dugo M, Callari M, Bongarzone I (2013) Bioinformatics tools for secretome analysis. Biochim Biophys Acta 1834(11):2442–2453PubMedCrossRefGoogle Scholar
  4. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi:10.1186/1471-2105-10-421 PubMedCentralPubMedCrossRefGoogle Scholar
  5. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2(4):953–971PubMedCrossRefGoogle Scholar
  6. Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34(Database issue):D247-251CrossRefGoogle Scholar
  7. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29-37CrossRefGoogle Scholar
  8. Fonzi WA (2009) The protein secretory pathway of Candida albicans. Mycoses 52(4):291–303PubMedCrossRefGoogle Scholar
  9. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35(Web Server issue):W585-587CrossRefGoogle Scholar
  10. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580PubMedCrossRefGoogle Scholar
  11. Lum G, Min XJ (2011) FunSecKB: the Fungal Secretome KnowledgeBase. Database: bar001. doi:10.1093/database/bar001
  12. Pierleoni A, Martelli PL, Casadio R (2008) PredGPI: a GPI-anchor predictor. BMC Bioinformatics 9:392 doi:10.1186/1471-2105-9-392 PubMedCentralPubMedCrossRefGoogle Scholar
  13. Rapoport TA (1992) Transport of proteins across the endoplasmic reticulum membrane. Science 258(5084):931-936PubMedCrossRefGoogle Scholar
  14. Sorgo AG, Heilmann CJ, Brul S, de Koster CG, Klis FM (2013) Beyond the wall: Candida albicans secret(e)s to survive. FEMS Microbiol Lett 338(1):10–17PubMedCrossRefGoogle Scholar
  15. Wymelenberg AV, Sabat G, Martinez D, Rajangam AS, Teeri TT, Gaskell J, Kersten PJ, Cullen D (2005) The Phanerochaete chrysosporium secretome: database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium. J Biotechnol 118(1):17–34PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Ana R. Cortázar
    • 1
  • Ana M. Aransay
    • 1
  • Manuel Alfaro
    • 2
  • José A. Oguiza
    • 2
  • José L. Lavín
    • 1
  1. 1.Genome Analysis PlatformCIC bioGUNE and CIBERehdDerioSpain
  2. 2.Department of Agrarian Production, Genetics and Microbiology Research GroupPublic University of NavarrePamplonaSpain

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