-
1
-
-
77950456427
-
Multiple personal genomes await
-
Venter JC: Multiple personal genomes await. Nature 2010, 464:676-677.
-
(2010)
Nature
, vol.464
, pp. 676-677
-
-
Venter, J.C.1
-
3
-
-
84857860662
-
GReEn: A tool for efficient compression of genome resequencing data
-
Pinho AJ, Pratas D, Garcia SP: GReEn: a tool for efficient compression of genome resequencing data. Nucl Acids Res 2012, 40(4):e27.
-
(2012)
Nucl Acids Res
, vol.40
, Issue.4
, pp. e27
-
-
Pinho, A.J.1
Pratas, D.2
Garcia, S.P.3
-
4
-
-
84876759103
-
A compression model for DNA multiple sequence alignment blocks
-
Matos LMO, Pratas D, Pinho AJ: A compression model for DNA multiple sequence alignment blocks. IEEE Trans Info Theory 2013, 59(5):3189-3198.
-
(2013)
IEEE Trans Info Theory
, vol.59
, Issue.5
, pp. 3189-3198
-
-
Matos, L.M.O.1
Pratas, D.2
Pinho, A.J.3
-
5
-
-
84871199924
-
Compression of next-generation sequencing reads aided by highly efficient de novo assembly
-
Jones DC, Ruzzo WL, Peng X, Katze MG: Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucl Acids Res 2012, 40(22):e171.
-
(2012)
Nucl Acids Res
, vol.40
, Issue.22
, pp. e171
-
-
Jones, D.C.1
Ruzzo, W.L.2
Peng, X.3
Katze, M.G.4
-
6
-
-
84875363204
-
Compression of FASTQ and SAM format sequencing data
-
Bonfield JK, Mahoney MV: Compression of FASTQ and SAM format sequencing data. PLoS ONE 2013, 8(3):e59190.
-
(2013)
PLoS ONE
, vol.8
, Issue.3
-
-
Bonfield, J.K.1
Mahoney, M.V.2
-
8
-
-
79955554401
-
Efficient storage of high throughput DNA sequencing data using reference-based compression
-
Fritz MHY, Leinonen R, Cochrane G, Birney E: Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res 2011, 21:734-740.
-
(2011)
Genome Res
, vol.21
, pp. 734-740
-
-
Fritz, M.H.Y.1
Leinonen, R.2
Cochrane, G.3
Birney, E.4
-
9
-
-
84861760100
-
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
-
Cox AJ, Bauer MJ, Jakobi T, Rosone G: Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics 2012, 28(11):1415-1419.
-
(2012)
Bioinformatics
, vol.28
, Issue.11
, pp. 1415-1419
-
-
Cox, A.J.1
Bauer, M.J.2
Jakobi, T.3
Rosone, G.4
-
10
-
-
84860994058
-
Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data
-
Qiao D, Yip WK, Lange C: Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. BMC Bioinformatics 2012, 13:100-107.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 100-107
-
-
Qiao, D.1
Yip, W.K.2
Lange, C.3
-
11
-
-
77951226627
-
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
-
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucl Acids Res 2010, 38(6):1767-1771.
-
(2010)
Nucl Acids Res
, vol.38
, Issue.6
, pp. 1767-1771
-
-
Cock, P.J.A.1
Fields, C.J.2
Goto, N.3
Heuer, M.L.4
Rice, P.M.5
-
12
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 1997, 13(3):235-238.
-
(1997)
Bioinformatics
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
13
-
-
0031634714
-
Sequence analysis using GCG
-
Butler BA: Sequence analysis using GCG. Methods Biochem Anal 1998, 39:74-97.
-
(1998)
Methods Biochem Anal
, vol.39
, pp. 74-97
-
-
Butler, B.A.1
-
14
-
-
0033500894
-
Shufflet: Shuffling sequences while conserving the k-let counts
-
Coward E: Shufflet: shuffling sequences while conserving the k-let counts. Bioinformatics 1999, 15(12):1058-1059.
-
(1999)
Bioinformatics
, vol.15
, Issue.12
, pp. 1058-1059
-
-
Coward, E.1
-
15
-
-
0043122944
-
ExPASy: The proteomics server for in-depth protein knowledge and analysis
-
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel R, Bairoch A: ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucl Acids Res 2003, 31(13):3784-3788.
-
(2003)
Nucl Acids Res
, vol.31
, Issue.13
, pp. 3784-3788
-
-
Gasteiger, E.1
Gattiker, A.2
Hoogland, C.3
Ivanyi, I.4
Appel, R.5
Bairoch, A.6
-
16
-
-
33749425231
-
RANDNA: A random DNA sequence generator
-
Piva F, Principato G: RANDNA: a random DNA sequence generator. Silico Biol 2006, 6(3):253-258.
-
(2006)
Silico Biol
, vol.6
, Issue.3
, pp. 253-258
-
-
Piva, F.1
Principato, G.2
-
17
-
-
33745610177
-
GenRGenS: Software for generating random genomic sequences and structures
-
Ponty Y, Termier M, Denise A: GenRGenS: software for generating random genomic sequences and structures. Bioinformatics 2006, 22(12):1534-1535.
-
(2006)
Bioinformatics
, vol.22
, Issue.12
, pp. 1534-1535
-
-
Ponty, Y.1
Termier, M.2
Denise, A.3
-
18
-
-
34548385781
-
RMotifGen: Random motif generator for DNA and protein sequences
-
Rouchka E, Hardin C: rMotifGen: random motif generator for DNA and protein sequences. BMC Bioinformatics 2007, 8:292.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 292
-
-
Rouchka, E.1
Hardin, C.2
-
19
-
-
80052209762
-
DNA synthetic sequences generation using multiple competing Markov models
-
Nice, France
-
Pratas D, Bastos CAC, Pinho AJ, Neves AJR, Matos L: DNA synthetic sequences generation using multiple competing Markov models. In Proc. of the IEEE Workshop on Statistical Signal Processing, Nice, France:2011.
-
(2011)
Proc. of the IEEE Workshop on Statistical Signal Processing
-
-
Pratas, D.1
Bastos, C.A.C.2
Pinho, A.J.3
Neves, A.J.R.4
Matos, L.5
-
20
-
-
76249133940
-
DNA sequences generated by BCH codes over GF(4)
-
Faria LCB, Rocha ASL, Kleinschmidt JH, Palazzo R, Silva-Filho Jr MC: DNA sequences generated by BCH codes over GF(4). Electron Lett 2010, 46(3):202-203.
-
(2010)
Electron Lett
, vol.46
, Issue.3
, pp. 202-203
-
-
Faria, L.C.B.1
Rocha, A.S.L.2
Kleinschmidt, J.H.3
Palazzo, R.4
Silva-Filho, M.C.5
-
21
-
-
84894478780
-
Uniform and non-uniform random generation of RNA secondary structures with pseudoknots
-
Montreal, Canada
-
Saule C, Wallon C, Denise A: Uniform and non-uniform random generation of RNA secondary structures with pseudoknots. In GASCOM, Montreal, Canada; 2010.
-
(2010)
GASCOM
-
-
Saule, C.1
Wallon, C.2
Denise, A.3
-
22
-
-
78650492254
-
An evolutionary model of DNA substring distribution
-
Edited by Elomaa T, Mannila H, Orponen P, Springer Berlin/Heidelberg
-
Kull M, Tretyakov K, Vilo J: An evolutionary model of DNA substring distribution. In Algorithms and Applications, Volume 6060 of Lecture Notes in Computer Science. Edited by Elomaa T, Mannila H, Orponen P, Springer Berlin/Heidelberg; 2010:147-157.
-
(2010)
Algorithms and Applications, Volume 6060 of Lecture Notes in Computer Science
, pp. 147-157
-
-
Kull, M.1
Tretyakov, K.2
Vilo, J.3
-
23
-
-
54949137701
-
MetaSim - A sequencing simulator for genomics and metagenomics
-
Richter DC, Ott F, Auch AF, Schmid R, Huson DH: MetaSim - a sequencing simulator for genomics and metagenomics. PLoS ONE 2008, 3(10):e3373.
-
(2008)
PLoS ONE
, vol.3
, Issue.10
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
Schmid, R.4
Huson, D.H.5
-
24
-
-
77956543003
-
Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim
-
Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I: Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 2010, 26(18):i420-i425.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
, pp. i420-i425
-
-
Balzer, S.1
Malde, K.2
Lanzén, A.3
Sharma, A.4
Jonassen, I.5
-
25
-
-
79956044149
-
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
-
Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF: Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245.
-
(2011)
BMC Genomics
, vol.12
, pp. 245
-
-
Gilles, A.1
Meglecz, E.2
Pech, N.3
Ferreira, S.4
Malausa, T.5
Martin, J.F.6
-
26
-
-
80052226692
-
Sequence-specific error profile of Illumina sequencers
-
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S: Sequence-specific error profile of Illumina sequencers. Nucl Acids Res 2011, 39(13):e90-e90.
-
(2011)
Nucl Acids Res
, vol.39
, Issue.13
, pp. e90-e90
-
-
Nakamura, K.1
Oshima, T.2
Morimoto, T.3
Ikeda, S.4
Yoshikawa, H.5
Shiwa, Y.6
Ishikawa, S.7
Linak, M.C.8
Hirai, A.9
Takahashi, H.10
Altaf-Ul-Amin, M.11
Ogasawara, N.12
Kanaya, S.13
-
27
-
-
84857145150
-
ART: A next-generation sequencing read simulator
-
Huang W, Li L, Myers JR, Marth GT: ART: a next-generation sequencing read simulator. Bioinformatics 2011, 28(4):593-594.
-
(2011)
Bioinformatics
, vol.28
, Issue.4
, pp. 593-594
-
-
Huang, W.1
Li, L.2
Myers, J.R.3
Marth, G.T.4
-
28
-
-
84856988681
-
GemSIM: General, error-model based simulator of next-generation sequencing data
-
McElroy K, Luciani F, Thomas T: GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics 2012, 13:74.
-
(2012)
BMC Genomics
, vol.13
, pp. 74
-
-
McElroy, K.1
Luciani, F.2
Thomas, T.3
-
29
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
30
-
-
79955375811
-
An automated homology-based approach for identifying transposable elements
-
Kennedy R, Unger M, Christley S, Collins F, Madey G: An automated homology-based approach for identifying transposable elements. BMC Bioinformatics 2011, 12:130+.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 130
-
-
Kennedy, R.1
Unger, M.2
Christley, S.3
Collins, F.4
Madey, G.5
-
31
-
-
84894435382
-
Detecting structural variants involving repetitive elements: Capturing transposition events of IS elements in the genome of Escherichia coli
-
Lee H, Popodi E, Foster PL, Tang H: Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli. BMC Bioinformatics 2012, 13(S-18):A12.
-
(2012)
BMC Bioinformatics
, vol.13 S-18
, pp. A12
-
-
Lee, H.1
Popodi, E.2
Foster, P.L.3
Tang, H.4
-
32
-
-
75949102506
-
Genome analysis with inter-nucleotide distances
-
Afreixo V, Bastos CAC, Pinho AJ, Garcia SP, Ferreira PJSG: Genome analysis with inter-nucleotide distances. Bioinformatics 2009, 25(23):3064-3070.
-
(2009)
Bioinformatics
, vol.25
, Issue.23
, pp. 3064-3070
-
-
Afreixo, V.1
Bastos, C.A.C.2
Pinho, A.J.3
Garcia, S.P.4
Ferreira, P.J.S.G.5
-
33
-
-
84896690677
-
DNA sequences at a Glance
-
Pinho AJ, Garcia SP, Pratas D, Ferreira PJSG: DNA sequences at a Glance. PLOS ONE 2013, 8(11):e79922.
-
(2013)
PLOS ONE
, vol.8
, Issue.11
-
-
Pinho, A.J.1
Garcia, S.P.2
Pratas, D.3
Ferreira, P.J.S.G.4
-
35
-
-
0033630766
-
Sequence complexity for biological sequence analysis
-
Allison L, Stern L, Edgoose T, Dix TI: Sequence complexity for biological sequence analysis. Computers & Chemistry 2000, 24:43-55.
-
(2000)
Computers & Chemistry
, vol.24
, pp. 43-55
-
-
Allison, L.1
Stern, L.2
Edgoose, T.3
Dix, T.I.4
-
36
-
-
84863762407
-
Symbolic to numerical conversion of DNA sequences using finite-context models
-
Barcelona, Spain
-
Pinho AJ, Pratas D, Ferreira PJSG, Garcia SP: Symbolic to numerical conversion of DNA sequences using finite-context models. In Proc. of the 19th European Signal Processing Conf, EUSIPCO-2011, Barcelona, Spain, 2011.
-
(2011)
Proc. of the 19th European Signal Processing Conf, EUSIPCO-2011
-
-
Pinho, A.J.1
Pratas, D.2
Ferreira, P.J.S.G.3
Garcia, S.P.4
-
39
-
-
84871807049
-
NGC: Lossless and lossy compression of aligned high-throughput sequencing data
-
Popitsch N, Haeseler A: NGC: lossless and lossy compression of aligned high-throughput sequencing data. Nucl Acids Res 2013, 41 (1):e27.
-
(2013)
Nucl Acids Res
, vol.41
, Issue.1
, pp. e27
-
-
Popitsch, N.1
Haeseler, A.2
|