Pfam domains

The detection of Pfam domains is done using the HMM profiles downloaded from Pfam server, HMMER3 software and PfamScan tools with E-value threshold of 0.001.

The output of PfamScan is presented in the Pfam domains table, where Nuc. Chains are chains of nucleic acid that have any kind of interaction with the corresponding domain. A user can also download the structure of the Pfam domain with the part of interacting nucleic acid in PDB format or visualize it with Jmol.