I have two genome assemblies of the same non-model species, call them Assembly 1 (generated from Illumina data) and Assembly 2 (generated from PacBio data).
For Assembly 1, I also have predicted proteome data, generated with EVM. Say there is a protein, call it Protein X, for which I have the fasta sequence from predictions, but suspect an error in Assembly 1 (because the Protein X has a long segment of auto-identity). For this reason, I would like to verify the assembly of the locus coding for Protein X in Assembly 2 and/or verify the presence of Protein X in the Assembly 2.
Data in my possession:
- both genome assemblies (fasta)
- raw rna-seq data
- reference-based transcriptome assembly for each genome assembly (fasta/gtf)
- set of predicted protein sequence based on Assembly 1 (fasta)
Things I was thinking of:
- build the EVM predictions on the Assembly 2 and verify the identity of Protein X by simple fasta identity check
- look for the protein sequence in the Assembly 2. I could use something similar to Reverse Translate to get the most likely nucleotide sequence from the input amino-acid sequence of Protein X, then align it to the Assembly 2 to check the coordinates of the locus it originates from - but I am not very sure of the relevance and/or correctness of this procedure
- something allowing 'blast' of the protein sequence in the Assembly 2 (but I am not aware of any software that could do that)
Any ideas on how I could do that?