We have observed a conserved gene order in three species of diatoms (algae) for a gene family of interest. A reviewer asked us to check this order also in a species which only has a partially assembled genome (Thalassiosira oceanica). This 'genome' consists out of 50k sequences with lengths between 500 and 5000bp.
I tried to run blastn using a 10.000bp fragment containing the 2 genes in sequence from a related species but no hits were returned. When I run tblastx however I get back 10 fragments, and I get the same result when using blastx and the two protein sequences on the 10.000bp fragment.
Now for my question:
Is there any program which allows me to try and map these 10 sequences on this presumably syntenic region?