Synteny / homology search tool

[hbn]

Hi there,

In a genome sequencing project of a plant species, we have obtained a large genomic scaffold (100 - 200 kb) for which we want to find a homologous fragment in Arabidopsis.

Of course I could do this through BLAST, but then I would probably get many many short hits and I just want to find a long fragment with high similarity.

Does anyone have any experience with this? Is there some kind of tool for this or procedure how to best approach this?

Thanks in advance!

[GenoMax]

Since you have no suggestions so far I will mention Mauve. If you know the chromosome from Arbidopsis that this may be homologous to then you could run it against that instead of the entire genome. Make sure there is enough RAM available.