As the size of biological sequence databases continues to grow, the time to search these databases has grown proportionally. This has led to many parallel implementations of common sequence analysis suites. However, it has become clear that many of these parallel sequence analysis tools do not scale well for medium to large-sized clusters. In this paper we describe an enhanced version of MPI-HMMER. We improve on MPI-HMMER's scalability through the use of parallel I/O and a parallel file system. Our enhancements to the core HMMER search tools, hmmsearch and hmmpfam, allows for scalability through 256 nodes where MPI-HMMER was previously limited to 64 nodes.