Changes between Version 22 and Version 23 of SatelliteUseCases

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Timestamp:
2009/03/20 14:57:29 (15 years ago)
Author:
shuichi
Comment:

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  • SatelliteUseCases

    v22 v23  
    5858== Results == 
    5959   
     60 
     61Question 
     62- Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. 
     63- For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. 
     64Answer 
     65- Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. 
     66- BioMart format is simple. 
     67 
     68 
     69Takeshi present an example 
     70- minor animal (ex, H.roretzi, closest animal of Ciona) 
     71- how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. 
     72- type of data is ESTs, assembled EST cluster,,,etc,, 
     73- potential flow: BioMart -> ANNOTATOR -> TogoDB 
     74 
     75[[Image(bh2009-usecase_1.pdf)]] 
     76 
    6077'''*SNPs data'''[[BR]] 
    6178 
     
    6582-can link dbSNPs to Galaxy for further analysis 
    6683 
     84[[Image(bh2009-usecase_2.pdf)]] 
    6785 
    6886'''*Multifasta format (amino acid sequences)'''[[BR]] 
     
    8199'''*Genome data'''[[BR]] 
    82100 
    83 Question 
    84 - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. 
    85 - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. 
    86 Answer 
    87 - Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. 
    88 - BioMart format is simple. 
    89  
    90  
    91 Takeshi present an example 
    92 - minor animal (ex, H.roretzi, closest animal of Ciona) 
    93 - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. 
    94 - type of data is ESTs, assembled EST cluster,,,etc,, 
    95 - potential flow: BioMart -> ANNOTATOR -> TogoDB 
    96  
    97 [[Image(bh2009-usecase.pdf)]] 
    98101 
    99102DL ESTs of Halocynthia roretzi from NCBI/Taxonomy