| | 1 | |
| | 2 | '''Log''' |
| | 3 | |
| | 4 | Data |
| | 5 | -SNPs, Affy provided by Prof.Kim |
| | 6 | SNPs data come from Affymatrix chip of stroke patients and normal people (contain 262,338 SNPs) |
| | 7 | |
| | 8 | - ANNOTATOR currently cannot analyse on SNPs data directly |
| | 9 | - Galaxy (http://galaxy.esphealth.org/) RGenetics |
| | 10 | quality control, ancestry and case-control analysis |
| | 11 | - BioMart |
| | 12 | |
| | 13 | BioMart |
| | 14 | - have to know dataset, filter, attribute |
| | 15 | - can use Perl API,.. |
| | 16 | - Martview |
| | 17 | - DAS access |
| | 18 | - Martview |
| | 19 | - can set up server and use in-house |
| | 20 | |
| | 21 | Question |
| | 22 | - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. |
| | 23 | - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. |
| | 24 | Answer |
| | 25 | - Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. |
| | 26 | - BioMart format is simple. |
| | 27 | |
| | 28 | |
| | 29 | Takeshi present |
| | 30 | - minor animal (closet animal Ciona) |
| | 31 | - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. |
| | 32 | - type of data is ESTs, assembled EST cluster,,,etc,, |
| | 33 | - potential flow: BioMart -> ANNOTATOR -> TogoDB |
| | 34 | |
| | 35 | DL ESTs of Halocynthia roretzi from NCBI/Taxonomy |
| | 36 | |
| | 37 | TogoDB by Toshiaki |
| | 38 | - upload table format (table services for uploading data will be able to access using WS) |
| | 39 | |
| | 40 | |
| | 41 | jORCA by Oswaldo |
| | 42 | |
| | 43 | -mapped WABI services |
| | 44 | - jORCA: WABI WSDL application can run in local machine after installation |
| | 45 | - jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, |
| | 46 | if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org |
| | 47 | *Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format) |
| | 48 | |
| | 49 | |
| | 50 | ANNOTATOR |
| | 51 | |
| | 52 | - how different between ANNOTATOR and InterProscan |
| | 53 | - how can I know the version of each DB use in Prim-seq-algorithm |
| | 54 | - it would be nice if user can save result in xml format |
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