Fungal Genome Tools discussion as Asilomar

For those of you building tools or heavily accessing fungal genome data, I am working to try and collect more resources about what is available and help coordinate access to common datasets. To this end I have organized a lunchtime session at the 2011 Fungal Genetics conference at Asilomar with the participation of several groups who provide genome browsers and data mining tools. The session is currently scheduled for the lunch on Friday, March 18 for those going to the conference.

There is also a mailing list to coordinate the topics in the session.  I am hoping the list will be a place for dialogues to share ideas, information about fungal genomics resources, and eventually better coordination of access to tools and data for the community.

 

3 thoughts on “Fungal Genome Tools discussion as Asilomar”

  1. As we could not reach the Asilomar meeting, I take the opportunity by the link to talk about our work for annotation the various ligninases from ongoing genome project. FOLy (Fungal Oxidative Lignin enzymes, http://foly-db.esil.univ-mrs.fr/) was developed in our Department (INRA UMR 1163) in 2008 and contains over 3800 entries semi-automatically annotated. FOLy was used to annotate and compare different filamentous fungi (Fung Genet Biol, Levasseur A. et al. 2008), including very recently, Schizophyllum commune (Nat Biotech, Ohm R. et al. 2010) or transcripts originating from specific ecosystems (Kellner H., PLoS One 2010).

    In our unit, our aim is to research the enzymatic potential of natural fungal biodiversity for degrading lignocellulosic biomass :
    – via the exploration by high-throughput screening of the fungal biodiversity grown on natural and synthetic substrates (CIRM fungal collection http://cirm.esil.univ-mrs.fr/);
    – via the genome analysis through the FOLy database (A. Levasseur and E. Record, INRA) that is both complementary and independent to CAZy database (we collaborate with P. Coutinho et B. Henrissat, CNRS, for several years)
    – in addition, our Department develops research on the specific model of biotechnological interest Pycnoporus cinnabarinus.

    I would therefore like to express our interest and our complete avaibility to participate in a network of experts for any ongoing or future projects. We showed our efficiency and expertise during the annotation and the writing of the paper dedicated to Schizophyllum commune (coordination, Han Wösten) and we will participate in the annotation process of several Aspergilli of biotechnological interest (coordination, Ronald de Vries).

    Our expertise and what we could bring in your projects:

    – Detailed annotation of FOLymes in families (LO and LDA) and sub-families as follows, with details on candidate and related enzymes :
    LO1 : laccase and more generally, MCO
    LO2 : manganese, lignin, versatile peroxidases, chloroperoxidases, dye-decolorizing peoxidases
    LO3 : cellobiose deshydrogenase (CDH)

    LDA 1 : aryl-alcohol oxidase
    LDA 2 : vanillyl-alcohol oxidase
    LDA 3 : glyoxal oxidase
    LDA 4 : pyranose oxidase
    LDA 5 : galactose oxidase
    LDA 6 : glucose oxidase
    LDA 7 : benzoquinone reductase
    LDA 8 : alcohol oxidase

    EST : cinnamoyl esterase, chlorogenate esterase, glucuronoyl esterase

    – We have had interest in characterizing the biochemical, molecular properties and the potential biotechnological applications of these enzymes for several years and most recently of esterases. So, we can give additional information to the annotation of these families.

    – Furthermore, we are also interested in the evolution of gene families through the analysis of genes under positive selection (dN / dS analysis) (BMC Evol Biol, Levasseur et al. 2006).

    – We are looking for new molecular markers to study phylogenetic relationships within the fungal kingdom.

    – Another point concerns the study of fungal genome rearrangements (synteny searches) between closely related species (Cassiope).

    We are looking forward to hearing from you.
    With our best regards,

    Anthony Levasseur and Eric Record

  2. Dear Sir/Madam,
    I was a user of the FOLY database. Unfortunately I cannot
    find it anymore. Does it has a new website?

    Yours Sincerely,

    Ing. Agr. Emiliano Jozami
    Cátedra de Biología,
    Parque Villarino, Zavalla, Santa Fe
    Facultad de Ciencias Agrarias,
    Universidad Nacional de Rosario

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