How to screen and select amino acid sequence with 2 motifs from the 30,000 fasta sequences?

Question

[Kiran]

I have around 30000 amino acid sequence from transcriptome, I am trying to screen then from with 2 motifs separated by 34 amino acid in one go, but I am not able to do it. Can anyone suggest me any software or online tool to perform this experiment. Thank you

Answer 1

[Elisabeth Gasteiger]

Have you tried ScanProsite at https://prosite.expasy.org/scanprosite ?

You can download the underlying tool from https://ftp.expasy.org/databases/prosite/ps_scan/ if you want to work with your local database instead of UniProtKB.