[BioC] Sequence analysis techniques in Bioconductor

[Javier Pérez Florido]

Dear list,
I would like to get the Arabidopsis thaliana protein functional 
relations extracted by standard sequence analysis techniques such as 
Phylogenetic profile, Rosetta Stone, Gene neighbor and Gene cluster. 
There is such information at the Prolinks database suitable for 
downloading, but the file is quite old (October, 2004).
I would like to know if there is a package in R that manages the access 
to the Prolinks database. In case there isn't, I don't know if there are 
Bioconductor packages that implement such sequence analysis techniques 
to get the most up-to-date information for this task.

Thanks in advance,
Javier