All 4 entries tagged Annotation

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November 18, 2009

H97 Genome Browser Portal Training

Gportal_thumb A two part training exercise in the use of the Agaricus bisporus var. bisporus H97 Genome Portal has been organised by the JGI. All collaborators involved in the H97 annotation effort are welcome to participate in the two 'dial-in' conference call sessions.

jgi_logo

  • Session I -- Mon, Nov 23, 8:00--9:30am Pacific Standard Time (16:00 -- GMT) will cover use of the Browser, Protein and Annotation pages
  • Session II -- Wed, Nov 25 (8:00am PST / 16:00 GMT) will cover the KEGG/KOG/GO browsers, track editor and the clustering tools

    Participants may find it beneficial to view the manual curation exercises available on the JGI pages <here>

    Collaborators who would like to take part in this training (and have not already registered) should contact Mike C in advance of the event for further instructions


    October 02, 2009

    Pre–release of Agaricus bisporus var. bisporus (H97) v1.0 genome assembly

    gbrowser_h97_20091002.jpg

    The JGI have announced the pre-release (or ‘internal’ release) of the Agaricus bisporus var. bisporus (H97) 8.50x  genome assembly following automated annotation.

    The H97 v1.0 genome browser is now available for community annotation inputs.

    In order to access the browser and make annotations, users will need to register with the JGI and the project team will need to approve the request.
    If you are interested in joining the annotation effort please contact the Agaricus genome team.

    Summary of A. bisporus var. bisporus H97 v1 assembly:
    Genome Size: 
    30.3 Mbp
    Total number of Scaffolds: 27
    Total number of EST clusters:           
    79,271
    Total number of trimmed ESTs:
    1,140,141
    JGI predicted 10,387 genes with the following average properties:
    Gene length (bp):                       
    1771.79
    Transcript length (bp):
    1413.32
    Protein length (aa): 426.20
    Exons per gene: 6.10
    Exon length (bp):
    232.25
    Intron length (bp): 
    71.72
    Genes were predicted by the following methods:
    EST-derived:                          
    3070 (29.6%)
    Homology-based:                   
    4242 (40.8%)
    ab initio:                              
    3075 (29.6%)
    Genes were validated by the following evidence:
    nr protein alignments:               
    8638 (83%)
    Pfam alignments: 
    5357 (52%)
    Completeness (5'M-3'*): 9376 (90%)

                     

    H97 JGI Project status http://bit.ly/9h4nS | Community annotation plans agaricusgenomeseqactivities_8

    June 15, 2009

    Annotation of Agaricus bisporus genome: community contributions

    JGI_20090615Sequence of the Agaricus bisporus H97 haploid genome (ca. 8.5 x coverage) is expected to enter a period of ‘hand-on’ community annotation within the next couple of months.
    Anybody interested in participating in the annotation effort should read our community circular genomecircular_20090615.pdf and contact MC for further information





    January 28, 2009

    JGI Fourth Annual User Meeting

    Writing about web page http://www.jgi.doe.gov/meetings/usermtg09/index.html

    The JGI have recently announced details of their 4th Annual User Meeting

    JGI_20090128Genomics of Energy & Environment

    U.S. Department of Energy / Joint Genome Institute (JGI)
    Marriott Hotel in Walnut Creek, California. March 25-27, 2009

    Significantly, the event includes a 'Eukaryotic Annotation Workshop' aimed at PIs and collaborators of eukaryotic projects with genomes annotated or expected for annotation in 2009, as well as new members of user communities interested in Community Annotation.

    http://www.jgi.doe.gov/meetings/usermtg09/index.html


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