Hi all,
I have assembled a genome (from illumina data) for a non-model species using allpaths and I'm searching for the mitochondria. I have a list of proteins (13 in total) that should be on mitochondria and have been unable to locate them in any sensible manner in this assembly(used the proteins with exonerate, spaln, blast and blat).
For example, blasting these proteins against the assembled genome reveals only one protein and I'm getting similar results with other approaches. I want to know why they are not showing up. I expect that the mitochondria should be assembled in a single contig (about 20kb in length) but it’s puzzling not even fragments are showing up.
Has anyone ever run into this problem with their assembly? Or does anyone have any idea what is going on here?
Any help would be appreciated.
Thanks and regards,
Ram
I have assembled a genome (from illumina data) for a non-model species using allpaths and I'm searching for the mitochondria. I have a list of proteins (13 in total) that should be on mitochondria and have been unable to locate them in any sensible manner in this assembly(used the proteins with exonerate, spaln, blast and blat).
For example, blasting these proteins against the assembled genome reveals only one protein and I'm getting similar results with other approaches. I want to know why they are not showing up. I expect that the mitochondria should be assembled in a single contig (about 20kb in length) but it’s puzzling not even fragments are showing up.
Has anyone ever run into this problem with their assembly? Or does anyone have any idea what is going on here?
Any help would be appreciated.
Thanks and regards,
Ram
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