Changes between Version 55 and Version 56 of SatelliteUseCases

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Timestamp:
2009/03/31 17:30:34 (9 years ago)
Author:
vachiranee
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  • SatelliteUseCases

    v55 v56  
    6565 
    6666Question 
    67 - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. 
     67- Takeshi asked about how to annotate in-house data by comparing with public genome data using BioMart. 
    6868- For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. 
    6969Answer 
     
    7272 
    7373 
    74 Takeshi present an example 
     74Takeshi presented an example 
    7575- minor animal (ex, H.roretzi, closest animal of Ciona) 
    7676- how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. 
     
    8181=== SNPs data === 
    8282 
    83 ANNOTATOR currently can not analyse SNPs data itself but can analyse genes data which contain SNPs of interested. [[BR]] 
     83ANNOTATOR currently can not analyse SNPs data itself but can analyze genes data which contain SNPs of interested. [[BR]] 
    8484Galaxy (http://galaxyproject.org) and RGenetics (http://rgenetics.org/) 
    8585        quality control, ancestry, case-control analysis, tdt, oter statistical tests[[BR]] 
     
    8989=== Multifasta format (amino acid sequences) === 
    9090 
    91 ANNOTATOR can upload multifasta format of amino acid sequences -> Prim-seq-an algorithm[[BR]]  
     91ANNOTATOR can upload multifasta format of amino acid sequences and do Prim-seq-an algorithm[[BR]]  
    9292BioMart can upload GeneID but not the sequences to retrieve information associated to the GeneID[[BR]] 
    93 jORCA provide list of analysis which can do with FASTA format[[BR]] 
     93jORCA provide list of analysis tools which could do with FASTA format[[BR]] 
    9494 
    9595 
    9696=== Multifasta format (nucleotide sequences) === 
    9797 
    98 ANNOTATOR can upload multifasta format of nucleotide sequences -> Prim-seq-an algorithm[[BR]] 
    99  
     98Currently, ANNOTATOR cannot analyze nucleotide sequences. 
    10099 
    101100DL ESTs of Halocynthia roretzi from NCBI/Taxonomy 
     
    110109-mapped WABI services 
    111110- jORCA: WABI WSDL application can run in local machine after installation 
    112 - jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, 
    113 if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org 
    114 *Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format) 
     111- jORCA can tell which kind of analysis tools can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, 
     112if put "FASTA" in Find box, the result come up with 23 tools that could use for analysis. For analysis use myexperiment.org [[BR]] 
     113*Magallanes: INB (Services that discover what kind of analysis can provide for your data format) 
    115114 
    116115== Results == 
     
    121120== TODOs == 
    122121 
    123  * How to combine the inhouse data into Public BioMart? => KAAS, blast2GO etc. 
     122 * How to combine the in house data into Public BioMart? => KAAS, blast2GO etc. 
    124123 * How easy to install the BioMart in local? 
    125124 * How modify the design of the interface of TogoDB?