How do I acertain synteny with a partially assembled genome

Question

[lijmstift]

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?

Answer 1

[Antonio R. Franco]

Give a try to MCScan

MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

[suren04]

Dear Franco, Regarding MCSCAN I have protein sequences of NBS gene family from Arabidopsis and Soybean. I also have gff file for both genomes including their genome sequences. My questions here are: Do I need to blast protein sequences of each genome against the genome of both Arabidopsis and Soybean? Or Do I just blast protein sequences of each genome against each other and against self? Or just the NBS family proteins. Can you please clarify how to work on this problem? Thanks for your help in advance. Also, what is that exact synteny_file , control_file in the manual? Can you please guide me on steps briefly?

Thank You