I'm working with two transcriptome assemblies. They're essentially different versions of the same transcriptome, one of them just includes more data and is therefore (presumably) better quality. A paper was published a couple of years ago with the old assembly, and we're now preparing a manuscript with the new assembly. We want to know which contigs from the old assembly correspond to which contigs from the new assembly.
I have the consensus sequence of all of the contigs from each assembly. I used the formatdb utility to create a BLAST database of the sequences from the old assembly, and then I BLASTed the sequences from the new assembly against this database. So now I just need to process the BLAST results and determine the relationship between contigs from one version to another.
I guess another way of putting it is that we want to determine the synteny between the two versions of the assembly.
Any suggestions about how to proceed?