SledgeHMMER

SledgeHMMER performs genome-scale searches of the Pfam database using a parallelized hmmpfam implementation of HMMER to identify Pfam HMM matches in protein sequence datasets.

Key Features:

• Parallel Processing: Implements a parallelized hmmpfam workflow capable of processing approximately 1.2 million sequences from Swiss-Prot and TrEMBL using 256 processors on IA64-based teragrid machines.
• Flexible Search Modes: Supports local, glocal, and merged search modes and allows selection between Pfam gathering thresholds or E-value thresholds for result filtering.
• Batch Processing: Accepts unrestricted batch input with no limitation on the number of query sequences for genome-scale analyses.
• Efficient Query Handling: Matches queries first against pre-calculated entries in the Pfam database and performs new searches for sequences with no pre-calculated matches.

Scientific Applications:

• Genomic and Proteomic Surveys: Enables large-scale Pfam annotation across whole-genome and proteome sequence sets.
• Functional Annotation: Facilitates identification of Pfam domains for protein functional annotation using Pfam HMM matches.
• Comparative and Evolutionary Analysis: Supports exploration of evolutionary relationships by scalable detection of conserved Pfam domains across large datasets.

Methodology:

Uses a parallelized version of hmmpfam (HMMER) with pre-calculated Pfam entries, configurable local/glocal/merged search modes, and selection of gathering or E-value thresholds, demonstrated on IA64-based teragrid parallel hardware.