Disease Resistance Analysis and Gene Orthology (DRAGO 2) is the second version of a pipeline to annotate resistance genes. DRAGO 2 can be launched on any transcriptome or proteome, thus the input can be either DNA or protein sequences in FASTA format. It detects LRR, Kinase, NBS and TIR domains from 60 HMM modules created for this purpose using HMMER v3 package and it is also able to detect CC and TM domains using COILS 2.2 and TMHMM 2.0c programs. As output, DRAGO 2 gives a table with the class of the query sequence and each domain found with the corresponding coordinates.