Searching InterPro with a batch of sequences

Often, people want to search InterPro with a batch of amino acid or nucleotide sequences — for example, to analyse whole genomes or proteomes. There are three ways in which it is possible to do this.

The first way is to submit a batch of amino acid or nucleotide sequences (up to 100) in fasta format to the InterPro search by sequence, either by pasting the sequences in the text box or by uploading a fasta file containing the sequences. In the InterProScan Search Results (Sequences) page, actions allow to delete, save, re-submit, and Download all the submitted sequences at once.

The second way involves downloading and installing the InterProScan analysis tool. The software comes with full installation instructions. It also has a lot of configurable features.

The third way of searching InterPro with a batch of sequences involves the use of EBI’s web services. These allow up to 1000 sequences to be analysed per request. We provide instructions on how to use the SOAP-based web service and the REST-based web service.