Synteny analysis from Transcriptome Data

[ElDonnis]

Dear All,

I'd like to perform a synteny analysis between transcriptome data (that can be retrived from EST database, microarray and RNA-seq experiments) of M.sativa , whose genome it's not sequenced, and M. truncatula genome. Is it possible? which program should i use?

Thanks

[mbayer]

Hi ElDonnis,

is the M. truncatula genome sequenced?

I would probably take the following approach for your sativa data:

1. De novo assembly of the RNASeq with e.g. Trinity
2. Meta-assembly of any existing ESTs and the contigs built form the RNASeq
3. Merge the resulting contigs and singlets into a single FASTA file
4. BLAST this against the truncatula sequences (if available) -- the top hit for each transcript should be the ortholog

cheers

Micha