Accelerated profile HMM searches
SR Eddy - PLoS computational biology, 2011 - journals.plos.org
Profile hidden Markov models (profile HMMs) and probabilistic inference methods have
made important contributions to the theory of sequence database homology search …
made important contributions to the theory of sequence database homology search …
The conceptual coupling metrics for object-oriented systems
D Poshyvanyk, A Marcus - 2006 22nd IEEE International …, 2006 - ieeexplore.ieee.org
Coupling in software has been linked with maintainability and existing metrics are used as
predictors of external software quality attributes such as fault-proneness, impact analysis …
predictors of external software quality attributes such as fault-proneness, impact analysis …
FPGA acceleration of the pair-HMMs forward algorithm for DNA sequence analysis
Many DNA sequence analysis tools have been developed to turn the massive raw DNA
sequencing data generated by NGS (Next Generation Sequencing) platforms into …
sequencing data generated by NGS (Next Generation Sequencing) platforms into …
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models
T Anderson, TJ Wheeler - BMC bioinformatics, 2024 - Springer
Background Sequence alignment lies at the heart of genome sequence annotation. While
the BLAST suite of alignment tools has long held an important role in alignment-based …
the BLAST suite of alignment tools has long held an important role in alignment-based …
Accelerating HMMer on FPGAs using systolic array based architecture
HMMer is a widely-used bioinformatics software package that uses profile HMMs (Hidden
Markov Models) to model the primary structure consensus of a family of protein or nucleic …
Markov Models) to model the primary structure consensus of a family of protein or nucleic …
Accelerating HMMER search using FPGA
T Takagi, T Maruyama - 2009 International Conference on Field …, 2009 - ieeexplore.ieee.org
This paper describes an implementation of HMMER with FPGA. HMMER is one of the most
used software tools for sensitive profile HMM (Hidden Markov Model) searches of biological …
used software tools for sensitive profile HMM (Hidden Markov Model) searches of biological …
Evaluating optimization strategies for hmmer acceleration on gpu
S Ferraz, N Moreano - 2013 International Conference on …, 2013 - ieeexplore.ieee.org
Comparing a biological sequence to a family of sequences is an important task in
Bioinformatics, commonly performed using tools such as HMMer. The Viterbi algorithm is …
Bioinformatics, commonly performed using tools such as HMMer. The Viterbi algorithm is …
Rapid RNA folding: analysis and acceleration of the Zuker recurrence
RNA folding is a compute-intensive task that lies at the core of search applications in
bioinformatics such as RNAfold and UNAFold. In this work, we analyze the Zuker RNA …
bioinformatics such as RNAfold and UNAFold. In this work, we analyze the Zuker RNA …
CUDA acceleration of P7Viterbi algorithm in HMMER 3.0
S Quirem, F Ahmed, BK Lee - 30th IEEE International …, 2011 - ieeexplore.ieee.org
Dynamic programming matrices and the P7Viterbi algorithm of HMMER 3.0 show high
parallelism in its code. Within the code, every query can have its score calculated in parallel …
parallelism in its code. Within the code, every query can have its score calculated in parallel …
High-Level synthesis of loops using the polyhedral model: the MMAlpha software
High-level synthesis (HLS) of loops allows efficient handling of intensive computations of an
application, eg in signal processing. Unrolling loops, the classical technique used in most …
application, eg in signal processing. Unrolling loops, the classical technique used in most …