[Gramene] Questions and suggestion for gramene

[pkuonline]

Dear Sir or Madam,

Recently I get engaged in one rice project. After some homework, I believe Gramene should be one of the best resources in this field, which seems to serve as Ensembl for Plant. But after browsing the web site, I am some confused in the following aspects:

1. Ensembl usually provides the fasta-format DNA/mRNA/protein sequence in the FASTA format of its FTP. For DNA sequence, it usually provide Repeat-Masked version and non masked version. But for Gramene, I found the directory is totally null as /pub/gramene/CURRENT_RELEASE/data/fasta .
2. Gramene provides the synteny map between japonica, rufipogon, maize and arabidopsis on the website. However, I can not find the corresponding dump on the ftp site. Could you tell me how to download the corresponding tables? Also the pipeline to generate the synteny is only briefly described in the help document. Could you give more details especially regarding rufipogon? This species seems to have no complete genome based on Gramene's document. 
3. Regarding syntenic map, Gramene does not provide the map between japonica and indica. Does this mean both sub-species is too similar and has no any structural change? 
4. Gramene used RepeatMasker and one repeat database of MIPS. But TIGR uses a totally different pipeline in this issue. Could you give some comments on annotation of repeat elements?

Finally, as a suggestion, Gramene provide a mail list as UCSC does. However, this mail list does not provide search function, which might be helpful for users to check whether the question of interest has been discussed already. 

Also may Gramene get better and better in future, :-)
 				
Best regards,
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Yong Zhang
Ph.D, Research Scholar
Manyuan Long's Lab
University of Chicago