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HMMER
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or…
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20 relations
BLAST
BioSLAX
Bioinformatics
Forward algorithm
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Broader (1)
Computational science
Papers overview
Semantic Scholar uses AI to extract papers important to this topic.
2016
2016
Structural Modelling and Characterization of Target Specifics of Trypanosoma cruzi, Etiologic agent of Chagas Disease
Carlyle Ribeiro Lima
2016
Corpus ID: 89729946
Selon l'organisation mondiale de la sante, 21 pays d'Amerique Latine et notamment le Bresil sont touches par la maladie de Chagas…
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2012
2012
A novel efficient FPGA architecture for HMMER acceleration
M. I. N. Isa
,
K. Benkrid
,
T. Clayton
International Conference on Reconfigurable…
2012
Corpus ID: 15221880
In this paper, a novel efficient FPGA-based architecture for the acceleration of the hmmsearch tool for biological sequence-to…
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Highly Cited
2010
Highly Cited
2010
The paralax infrastructure: Automatic parallelization with a helping hand
Hans Vandierendonck
,
S. Rul
,
K. D. Bosschere
International Conference on Parallel…
2010
Corpus ID: 14979456
Speeding up sequential programs on multicores is a challenging problem that is in urgent need of a solution. Automatic…
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2010
2010
Hardware Acceleration of HMMER on FPGAs
Steven Derrien
,
P. Quinton
Journal of Signal Processing Systems
2010
Corpus ID: 15762579
We propose a new parallelization scheme for the hmmsearch function of the HMMER software, in order to target FPGA technology…
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2009
2009
Improving MPI-HMMER's scalability with parallel I/O
J. Walters
,
Rohan Darole
,
V. Chaudhary
IEEE International Symposium on Parallel…
2009
Corpus ID: 2536721
We present PIO-HMMER, an enhanced version of MPI-HMMER. PIO-HMMER improves on MPI-HMMER's scalability through the use of parallel…
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2009
2009
Accelerating HMMer on FPGAs using systolic array based architecture
Yanteng Sun
,
Peng Li
,
Guochang Gu
,
Y. Wen
,
Yuan Liu
,
Dong Liu
IEEE International Symposium on Parallel…
2009
Corpus ID: 939859
HMMer is a widely-used bioinformatics software package that uses profile HMMs (Hidden Markov Models) to model the primary…
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2007
2007
Preliminary results in accelerating profile HMM search on FPGAs
A. Jacob
,
J. Lancaster
,
J. Buhler
,
R. Chamberlain
IEEE International Parallel and Distributed…
2007
Corpus ID: 1881384
Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence…
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2007
2007
MPI-HMMER-Boost: Distributed FPGA Acceleration
J. Walters
,
Xiandong Meng
,
+5 authors
Joseph I. Landman
J. VLSI Signal Process.
2007
Corpus ID: 6035493
HMMER, based on the profile Hidden Markov Model (HMM) is one of the most widely used sequence database searching tools, allowing…
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Highly Cited
2006
Highly Cited
2006
Auto-pipe and the X language: a pipeline design tool and description language
M. Franklin
,
Eric J. Tyson
,
J. Buckley
,
P. Crowley
,
John Maschmeyer
Proceedings 20th IEEE International Parallel…
2006
Corpus ID: 12096452
Auto-Pipe is a tool that aids in the design, evaluation and implementation of applications that can be executed on computational…
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Highly Cited
2006
Highly Cited
2006
BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btl655 Structural bioinformatics Biskit—A software platform for structural bioinformatics
2006
Corpus ID: 16933629
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