P18: A Parallel Python Implementation of BLAST+ (PPIB)
for Characterization of Complex Microbial Consortia
SessionPoster Reception
Event Type
ACM Student Research Competition
Poster
Reception
TimeTuesday, November 14th5:15pm -
7pm
LocationFour Seasons Ballroom
DescriptionTechnological advancements in analytical
instrumentation have enabled large-scale data
acquisitions among the ‘-omics’ sciences of genomics,
transcriptomics, and proteomics. An essential
application among ‘-omics’ disciplines is the Basic
Local Alignment Search Tool (BLAST) for functional
inference of biomolecules. Though implementations of
BLAST+ have been modified to address data volume growth,
such improvements have neither been consistently
maintained for high performance computing (HPC), nor
have they been applied to complex microbiomes. Further,
such implementations do not scale well to microbiomes of
Naval interest on HPC systems in our hands.
Here, we compare 2 HPC implementations: BLAST+ and a Parallel Python Implementation of BLAST+ (PPIB) for protein functional inference. PPIB enabled functional inference of 2 complex microbiomes, which may be attributed to a combination of MPI and Python multiprocessing to query up to 3,600 proteins simultaneously. In contrast, BLAST+ did not complete functional assignments relative to PPIB at a comparable walltime.
Here, we compare 2 HPC implementations: BLAST+ and a Parallel Python Implementation of BLAST+ (PPIB) for protein functional inference. PPIB enabled functional inference of 2 complex microbiomes, which may be attributed to a combination of MPI and Python multiprocessing to query up to 3,600 proteins simultaneously. In contrast, BLAST+ did not complete functional assignments relative to PPIB at a comparable walltime.
