Changes between Version 55 and Version 56 of SatelliteUseCases
- Timestamp:
- 2009/03/31 17:30:34 (16 years ago)
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SatelliteUseCases
v55 v56 65 65 66 66 Question 67 - Takeshi asked about how to anno ate in-house data withcomparing with public genome data using BioMart.67 - Takeshi asked about how to annotate in-house data by comparing with public genome data using BioMart. 68 68 - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. 69 69 Answer … … 72 72 73 73 74 Takeshi present an example74 Takeshi presented an example 75 75 - minor animal (ex, H.roretzi, closest animal of Ciona) 76 76 - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. … … 81 81 === SNPs data === 82 82 83 ANNOTATOR currently can not analyse SNPs data itself but can analy se genes data which contain SNPs of interested. [[BR]]83 ANNOTATOR currently can not analyse SNPs data itself but can analyze genes data which contain SNPs of interested. [[BR]] 84 84 Galaxy (http://galaxyproject.org) and RGenetics (http://rgenetics.org/) 85 85 quality control, ancestry, case-control analysis, tdt, oter statistical tests[[BR]] … … 89 89 === Multifasta format (amino acid sequences) === 90 90 91 ANNOTATOR can upload multifasta format of amino acid sequences ->Prim-seq-an algorithm[[BR]]91 ANNOTATOR can upload multifasta format of amino acid sequences and do Prim-seq-an algorithm[[BR]] 92 92 BioMart can upload GeneID but not the sequences to retrieve information associated to the GeneID[[BR]] 93 jORCA provide list of analysis which cando with FASTA format[[BR]]93 jORCA provide list of analysis tools which could do with FASTA format[[BR]] 94 94 95 95 96 96 === Multifasta format (nucleotide sequences) === 97 97 98 ANNOTATOR can upload multifasta format of nucleotide sequences -> Prim-seq-an algorithm[[BR]] 99 98 Currently, ANNOTATOR cannot analyze nucleotide sequences. 100 99 101 100 DL ESTs of Halocynthia roretzi from NCBI/Taxonomy … … 110 109 -mapped WABI services 111 110 - 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 c an use for analysis. For analysis use myexperiment.org114 *Magallanes: INB (Services discoveringthat 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*, 112 if 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) 115 114 116 115 == Results == … … 121 120 == TODOs == 122 121 123 * How to combine the in house data into Public BioMart? => KAAS, blast2GO etc.122 * How to combine the in house data into Public BioMart? => KAAS, blast2GO etc. 124 123 * How easy to install the BioMart in local? 125 124 * How modify the design of the interface of TogoDB?
