Blast search for solanum pseudomolecules

Question

[agata88]

Hi all!

I am working on solanum tuberosum genes and I would like to identify sequences in Solanum Tuberosum pseudomolecules with the use of BLAST. As far as I know pseudomolecules are superscaffolds not included in ensemble reference genome. Where can I find the proper reference?

Best, Agata

Answer 1

[GenoMax]

pseudomolecules that is a new one for me. They seem to be available here.

[agata88]

It's new to me too. I was asked to check for pseudomolecules with the use of BLAST. I am wondering if I find my sequence in there, does it mean that it has copy of gene (pseudogene?) also loacated in superscaffolds?

[GenoMax]

pseudomolecules refers to the DNA sequence assembly for a chromosome/genome. There is more on this page. Perhaps you should get the sequences from there.

If you don't want to download locally there is an online blast server available.

[agata88]

Thanks, I used it and I have found a 100% identity to the input sequences, but I am not sure if I understand correctly ... does it mean that beside reference ensembl genome where my gene was annotated there is another copy on pseudomolecules reference? I am confused because it looks like all of my genes have another pseudomolecule copy ... and that is weird...

Answer 2

[agata88]

I have the answer: it can help identify extra copy of gene, not detected by ensmebl annotations. This copy of gene is without protein functionality.

Thank you!

Best,

Agata