Abstract
HMMer is a widely used tool for protein sequence homology detection, as well as functional annotation of homologous protein sequences, and protein family classification. The HMMer program is based upon a Viterbi algorithm coded in C, and is quite time consuming. Significant efforts have been undertaken to accelerate this program using custom special purpose hardware, as well as more recent attempts to leverage commodity special purpose hardware. This work will report on several minimally invasive code refactoring efforts independently undertaken by the authors, and their significant performance impact on wall clock execution time of the entire program for various test cases.
Keywords
Code refactoringComputer scienceLeverage (statistics)AnnotationOperating systemViterbi algorithmCode (set theory)Programming languageEmbedded systemParallel computingSoftwareHidden Markov modelArtificial intelligence
Affiliated Institutions
Related Publications
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on...
Scalable molecular dynamics with NAMD
Abstract NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end par...
Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable perform...
Functional and structural genomics using PEDANT
Abstract Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in rel...
Publication Info
- Year
- 2006
- Type
- article
- Volume
- it 13
- Pages
- 5 pp.-5 pp.
- Citations
- 14
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
14
OpenAlex
1
Influential
8
CrossRef
Cite This
Joseph Landman,
Jeffrey Ray,
John Paul Walters
(2006).
Accelerating HMMer searches on Opteron processors with minimally invasive recoding.
20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA'06)
, it 13
, 5 pp.-5 pp..
https://doi.org/10.1109/aina.2006.67
Identifiers
- DOI
- 10.1109/aina.2006.67