KPHMMER: Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes

Motivation Reinforcement of HMMER search for secondary metabolism-specific Pfam domains should contribute to discover novel biosynthetic machinery of clinically important natural products. Results Here we provide a Python-based command line tool, named as KPHMMER, to extract the Pfam domains that are specific in the user-defined set of pathways in the user-defined set of organisms registered in the KEGG database. KPHMMER outperformed the previous study in detecting secondary metabolism-specific Pfam domain set. Furthermore, it was proven that KPHMMER helps reduce the computational cost compared with the case using the whole Pfam-A HMM file. We believe that KPHMMER is a powerful tool enabling to deal with many other genome-sequenced species for more general purpose. Availability KPHMMER is implemented as a Python package freely available via the package management system “pip” and also at https://github.com/suecharo/KPHMMER Contact [email protected]