Hello everyone,
I'm currently analyzing mitochondrial sequences from different scorpion species, specifically comparing their protein-coding gene sequences to a reference scorpion sequence to detect potential variants. My aim is to check whether the identified variants might have an impact at the protein level, and for this I wanted to use PolyPhen-2. However, I'm facing a problem. PolyPhen-2 requires either a protein ID or an SNP identifier (such as from Ensembl or UniProtKB). Since I'm working with non-model organisms (e.g., Androctonus amoreuxi), I couldn’t find any protein or transcript identifiers corresponding to the sequences I'm analyzing. I tried inputting a FASTA protein sequence, but PolyPhen-2 does not seem to accept that format and I got this message (ERROR: BLAST search failed (no hits found in BLAST XML), giving up Alignment selection missing in XML)
Has anyone worked with non-model organisms or scorpion sequences and successfully used PolyPhen-2 or another tool to predict the functional impact of amino acid substitutions?
I would highly appreciate any suggestions, whether it’s about:
- How to retrieve a suitable protein ID from Ensembl, UniProt, or another database,
- Or any alternative tools better suited for variant effect prediction in non-model invertebrates.
Thanks a lot in advance for your help!
Best regards,
Hi,
If you're working with a non-model organism, you can manually perform a BLAST search using a closely related reference species — in this case, one that is phylogenetically close to the scorpion species. After the BLAST, you can assign the protein IDs from the reference organism to your species based on the best matches.
- Badges
- Science method