Satellite meeting for Use-cases development and documentation

Topics

Participants

• Toshiaki Katayama
• Young Joo Kim
• Keun-Joon Park
• Yunsun Nam
• Arek Kasprzyk
• Syed Haider
• Shuichi Kawashima
• Takeshi Kawashima
• Raoul JP Bonnal
• Tatsuya Nishizawa
• Oswaldo Trelles
• José M. Fernández
• Paul Gordon
• Vachiranee Limviphuvadh
• Tobias Gattermayer
• Riu Yamashita
• Fumikazu Konishi

Targets

Date

• 2009/3/19 15:00-18:00
• and anytime

Room

• 3F

Notes

Data for testing

1) SNPs data contain 262,338 SNPs (Stroke patient vs. normal) from Affymetrix GeneChip? (provided by Prof.Kim) 2) Multifasta format of amino acid sequences of 53 genes which are located at 4p15 (disease map locus of one form of epilepsy) (provided by Vachiranee) 3) Multifasta format of nucleotide sequences (provided by Riu) 4) Genome data (provided by Takeshi)

Software

1) BioMart 2) Galaxy 3) jORCA 4) ANNOTATOR

ANNOTATOR currently cannot analyse on SNPs data directly

• Galaxy ( http://galaxyproject.org) and RGenetics ( http://rgenetics.org/)

quality control, ancestry, case-control analysis, tdt, oter statistical tests

• BioMart

BioMart - have to know dataset, filter, attribute - can use Perl API,.. - Martview - DAS access - Martview - can set up server and use in-house

Question - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. Answer - Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. - BioMart format is simple.

Takeshi present - minor animal (closet animal Ciona) - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. - type of data is ESTs, assembled EST cluster_,etc - potential flow: BioMart -> ANNOTATOR -> TogoDB

DL ESTs of Halocynthia roretzi from NCBI/Taxonomy

TogoDB by Toshiaki - upload table format (table services for uploading data will be able to access using WS)

jORCA by Oswaldo

-mapped WABI services - jORCA: WABI WSDL application can run in local machine after installation - jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org *Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format)

ANNOTATOR

- how different between ANNOTATOR and InterProscan? - how can I know the version of each DB use in Prim-seq-algorithm - it would be nice if user can save result in xml format

Results

TODOs