Can I run DNA as well as protein sequences through InterProScan?
Due to resource limitations neither the EBI web interface nor web services for InterProScan will be accepting nucleotide sequence submissions until further notice. To process nucleotide sequences using InterProScan you first need to translate your nucleotide sequence using a tool such as Transeq, and then pick the relevant ORF translations for analysis. We recommend filtering the ORF translations by the following criteria: 1. Sequence length. Short sequences ( 2. Significant hits from sequence similarity searches. The signatures used by InterProScan are based on known protein sequences so a filtering step by performing a BLAST of FASTA sequence similarity search with the ORF translations against the UniProtKB or UniParc protein sequence databases and only keeping sequences which have hits with e-values The standalone version of InterProScan can perform the translation and ORF length filtering as part of the submission and is recommended if you need to perform large numbers of analysis
