-
1
-
-
79955767858
-
Exact and complete short read alignment to microbial genomes using GPU programming
-
Blom, J. et al. (2011) Exact and complete short read alignment to microbial genomes using GPU programming. Bioinformatics, 27, 1351-1358.
-
(2011)
Bioinformatics
, vol.27
, pp. 1351-1358
-
-
Blom, J.1
-
2
-
-
0003573193
-
-
Technical Report 124, Digital Equipment Corporation, Palo Alto, CA
-
Burrows, M. and Wheeler, D. J. (1994) A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation, Palo Alto, CA.
-
(1994)
A block sorting lossless data compression algorithm
-
-
Burrows, M.1
Wheeler, D.J.2
-
3
-
-
63549114801
-
PASS: a program to align short sequences
-
Campagna, D. et al. (2009) PASS: a program to align short sequences. Bioinformatics, 25, 967-968.
-
(2009)
Bioinformatics
, vol.25
, pp. 967-968
-
-
Campagna, D.1
-
4
-
-
0031978181
-
Base-calling of automated sequencer traces using phred
-
Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
-
(1998)
II. Error probabilities. Genome Res.
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
6
-
-
30544432152
-
Indexing compressed text
-
Ferragina, P. and Manzini, G. (2005) Indexing compressed text. J. ACM, 52, 4.
-
(2005)
J. ACM
, vol.52
, pp. 4
-
-
Ferragina, P.1
Manzini, G.2
-
7
-
-
33645796213
-
Compressed suffix arrays and suffix trees with applications to text indexing and string matching
-
Grossi, R. and Vitter, J. S. (2005) Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comput., 35, 2.
-
(2005)
SIAM J. Comput.
, vol.35
, pp. 2
-
-
Grossi, R.1
Vitter, J.S.2
-
8
-
-
70450177746
-
BFAST: an alignment tool for large scale genome resequencing
-
Homer, N. et al. (2009) BFAST: an alignment tool for large scale genome resequencing. PLoS One, 4, e7767.
-
(2009)
PLoS One
, vol.4
-
-
Homer, N.1
-
9
-
-
34547375123
-
Aspace and time efficient algorithm for constructing compressed suffix arrays
-
Hon, W. K. et al. (2007)Aspace and time efficient algorithm for constructing compressed suffix arrays. Algorithmica, 48, 23-36.
-
(2007)
Algorithmica
, vol.48
, pp. 23-36
-
-
Hon, W.K.1
-
10
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz, S. et al. (2004)Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
-
(2004)
Genome Biol
, vol.5
-
-
Kurtz, S.1
-
11
-
-
79951974373
-
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
-
Kuttippurathu, L. et al. (2011) CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics, 27, 715-717.
-
(2011)
Bioinformatics
, vol.27
, pp. 715-717
-
-
Kuttippurathu, L.1
-
12
-
-
40749108125
-
Compressed indexing and local alignment of DNA
-
Lam, T. W. et al. (2008) Compressed indexing and local alignment of DNA. Bioinformatics, 24, 791-797.
-
(2008)
Bioinformatics
, vol.24
, pp. 791-797
-
-
Lam, T.W.1
-
13
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
-
14
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
-
15
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
16
-
-
67649884743
-
Fast and accurate short read alignment with Burrows- Wheeler transform
-
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics, 25, 1755-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1755-1760
-
-
Li, H.1
Durbin, R.2
-
17
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows- Wheeler transform
-
Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics, 26, 589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
18
-
-
40049104732
-
SOAP: short oligonucleotide alignment program
-
Li, R. et al. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
-
19
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
Li, R. et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
-
20
-
-
44849137198
-
NVIDIATesla: a unified graphics and computing architecture
-
Lindholm, E. et al. (2008) NVIDIATesla: a unified graphics and computing architecture. IEEE Micro, 28, 39-55.
-
(2008)
IEEE Micro
, vol.28
, pp. 39-55
-
-
Lindholm, E.1
-
21
-
-
74549205661
-
CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
-
Liu, Y. et al. (2009) CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res. Notes, 2, 73.
-
(2009)
BMC Res. Notes
, vol.2
, pp. 73
-
-
Liu, Y.1
-
22
-
-
77956339477
-
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
-
Liu, Y. et al. (2010) CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognit. Lett., 31, 2170-2177.
-
(2010)
Pattern Recognit. Lett.
, vol.31
, pp. 2170-2177
-
-
Liu, Y.1
-
23
-
-
79953095545
-
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
-
Liu, Y. et al. (2011) DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinformatics, 12, 85.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 85
-
-
Liu, Y.1
-
24
-
-
77951900491
-
-
NVIDIA. NVIDIA Corporation Whitepaper
-
NVIDIA (2009) NVIDIA's next generation CUDA compute architecture: Fermi. NVIDIA Corporation Whitepaper. http://www.nvidia.com/content/PDF/fermi_white_papers/NVIDIA_Fermi_Compute_Architecture_Whitepaper pdf
-
(2009)
NVIDIA's next generation CUDA compute architecture: Fermi
-
-
-
25
-
-
67049159825
-
SHRiMP: accurate mapping of short color-space reads
-
Rumble, S. M. et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol., 5, e1000386.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Rumble, S.M.1
-
26
-
-
41249096306
-
Using quality scores and longer reads improves accuracy of Solexa read mapping
-
Smith, A. D. et al. (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9, 128.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 128
-
-
Smith, A.D.1
-
27
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F. and Waterman, M. S. (1998) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1998)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
28
-
-
78651415181
-
GPU-BLAST: using graphics processors to accelerate protein sequence alignment
-
Vouzis, P. D. and Sahinidis, N. V. (2010) GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics, 27, 182-188.
-
(2010)
Bioinformatics
, vol.27
, pp. 182-188
-
-
Vouzis, P.D.1
Sahinidis, N.V.2
|