-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Z. W. Miller, and D. L. DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25(17):3389-3402, 1997. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
67650735586
-
ABACAS: Algorithm-based automatic contiguation of assembled sequences
-
S. Assefa, T. M. Keane, T. D. Otto, C. Newbold, and M. Berriman. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25:1968-1969, 2009.
-
(2009)
Bioinformatics
, vol.25
, pp. 1968-1969
-
-
Assefa, S.1
Keane, T.M.2
Otto, T.D.3
Newbold, C.4
Berriman, M.5
-
3
-
-
0036144823
-
ARACHNE: A whole-genome shotgun assembler
-
DOI 10.1101/gr.208902
-
S. Batzoglou, D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger, J. P. Mesirov, and E. S. Lander. ARACHNE: a whole-genome shotgun assembler. Genome Res., 12:177-189, 2002. (Pubitemid 34070592)
-
(2002)
Genome Research
, vol.12
, Issue.1
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.B.2
Stanley, K.3
Butler, J.4
Gnerre, S.5
Mauceli, E.6
Berger, B.7
Mesirov, J.P.8
Lander, E.S.9
-
4
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
M. Boetzer, C. V. Henkel, H. J. Jansen, D. Butler, and W. Pirovano. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 27:578-579, 2011.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
5
-
-
43149086380
-
ALLPATHS: De novo assembly of whole-genome shotgun microreads
-
DOI 10.1101/gr.7337908
-
J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18:810-820, 2008. (Pubitemid 351645071)
-
(2008)
Genome Research
, vol.18
, Issue.5
, pp. 810-820
-
-
Butler, J.1
MacCallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
Lander, E.S.6
Nusbaum, C.7
Jaffe, D.B.8
-
6
-
-
0347724102
-
GRIL: Genome rearrangement and inversion locator
-
DOI 10.1093/bioinformatics/btg378
-
A. E. Darling, B. Mau, F. R. Blattner, and N. T. Perna. GRIL: genome rearrangement and inversion locator. Bioinformatics, 20(1):122-124, 2004. (Pubitemid 38088350)
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 122-124
-
-
Darling, A.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
7
-
-
3543051830
-
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
-
DOI 10.1101/gr.2289704
-
A. E. Darling, B. Mau, F. R. Blattner, and N. T. Perna. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res., 14:1394-1403, 2004. (Pubitemid 39029237)
-
(2004)
Genome Research
, vol.14
, Issue.7
, pp. 1394-1403
-
-
Darling, A.C.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
8
-
-
48249144818
-
Dynamics of genome rearrangement in bacterial populations
-
A. E. Darling, I. Miklós, and M. A. Ragan. Dynamics of genome rearrangement in bacterial populations. PLoS Genet., 4(7):e1000128, 2008.
-
(2008)
PLoS Genet.
, vol.4
, Issue.7
-
-
Darling, A.E.1
Miklós, I.2
Ragan, M.A.3
-
9
-
-
77954324418
-
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
-
A. Dayarian, T. P. Michael, and A. M. Sengupta. SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics, 11:345, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 345
-
-
Dayarian, A.1
Michael, T.P.2
Sengupta, A.M.3
-
10
-
-
58149527706
-
A genomic distance based on MUM indicates discontinuity between most bacterial species and genera
-
M. Deloger, M. El Karoui, and M. A. Petit. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J. Bacteriol., 191:91-99, 2009.
-
(2009)
J. Bacteriol.
, vol.191
, pp. 91-99
-
-
Deloger, M.1
El Karoui, M.2
Petit, M.A.3
-
11
-
-
0034568798
-
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
-
research
-
J. A. Eisen, J. F. Heidelberg, O. White, and S. L. Salzberg. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol., 1(6):research0011.1-0011.9, 2000.
-
(2000)
Genome Biol.
, vol.1
, Issue.6
, pp. 00111-00119
-
-
Eisen, J.A.1
Heidelberg, J.F.2
White, O.3
Salzberg, S.L.4
-
12
-
-
0141853948
-
PCAP: A whole-genome assembly program
-
DOI 10.1101/gr.1390403
-
X. Huang, J. Wang, S. Aluru, S. P. Yang, and L. Hillier. PCAP: a whole-genome assembly program. Genome Res., 13:2164-2170, 2003. (Pubitemid 37161773)
-
(2003)
Genome Research
, vol.13
, Issue.9
, pp. 2164-2170
-
-
Huang, X.1
Wang, J.2
Aluru, S.3
Yang, S.-P.4
Hillier, L.5
-
13
-
-
77949515650
-
R2cat: Synteny plots and comparative assembly
-
P. Husemann and J. Stoye. r2cat: synteny plots and comparative assembly. Bioinformatics, 26:570-571, 2010.
-
(2010)
Bioinformatics
, vol.26
, pp. 570-571
-
-
Husemann, P.1
Stoye, J.2
-
14
-
-
1242281253
-
The greedy path-merging algorithm for contig scaffolding
-
D. H. Huson, K. Reinert, and E. W. Myers. The greedy path-merging algorithm for contig scaffolding. J. ACM, 49:603-615, 2002.
-
(2002)
J. ACM
, vol.49
, pp. 603-615
-
-
Huson, D.H.1
Reinert, K.2
Myers, E.W.3
-
15
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
W. J. Kent. BLAT-the BLAST-like alignment tool. Genome Res., 12:656-664, 2002.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
16
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
S. Kurtz, A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. L. Salzberg. Versatile and open software for comparing large genomes. Genome Biol., 5(2):R12, 2004.
-
(2004)
Genome Biol.
, vol.5
, Issue.2
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
17
-
-
75349109607
-
ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads
-
I. Maccallum et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol., 10:R103, 2009.
-
(2009)
Genome Biol.
, vol.10
-
-
MacCallum, I.1
-
18
-
-
77953019477
-
Scaffold filling contig fusion and comparative gene order inference
-
A. Muñoz, C. Zheng, Q. Zhu, V. Albert, S. Rounsley and D. Sankoff. Scaffold Filling, Contig Fusion and Comparative Gene Order Inference. BMC Bioinformatics, 11:304, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 304
-
-
Muñoz, A.1
Zheng, C.2
Zhu, Q.3
Albert, V.4
Rounsley, S.5
Sankoff, D.6
-
19
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
DOI 10.1126/science.287.5461.2196
-
E. W. Myers et al.. A whole-genome assembly of Drosophila. Science, 287:2196-2204, 2000. (Pubitemid 30177014)
-
(2000)
Science
, vol.287
, Issue.5461
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
Dew, I.M.4
Fasulo, D.P.5
Flanigan, M.J.6
Kravitz, S.A.7
Mobarry, C.M.8
Reinert, K.H.J.9
Remington, K.A.10
Anson, E.L.11
Bolanos, R.A.12
Chou, H.-H.13
Jordan, C.M.14
Halpern, A.L.15
Lonardi, S.16
Beasley, E.M.17
Brandon, R.C.18
Chen, L.19
Dunn, P.J.20
Lai, Z.21
Liang, Y.22
Nusskern, D.R.23
Zhan, M.24
Zhang, Q.25
Zheng, X.26
Rubin, G.M.27
Adams, M.D.28
Venter, J.C.29
more..
-
20
-
-
43349084767
-
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
-
DOI 10.1093/bioinformatics/btn102
-
N. Nagarajan, T. D. Read, and M. Pop. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics, 24:1229-1235, 2008. (Pubitemid 351659618)
-
(2008)
Bioinformatics
, vol.24
, Issue.10
, pp. 1229-1235
-
-
Nagarajan, N.1
Read, T.D.2
Pop, M.3
-
21
-
-
0346505466
-
Hierarchical scaffolding with Bambus
-
DOI 10.1101/gr.1536204
-
M. Pop, D. S. Kosack, and S. L. Salzberg. Hierarchical scaffolding with Bambus. Genome Res., 14:149-159, 2004. (Pubitemid 38088536)
-
(2004)
Genome Research
, vol.14
, Issue.1
, pp. 149-159
-
-
Pop, M.1
Kosack, D.S.2
Salzberg, S.L.3
-
22
-
-
34547852218
-
OSLay: Optimal syntenic layout of unfinished assemblies
-
DOI 10.1093/bioinformatics/btm153
-
D. C. Richter, S. C. Schuster, and D. H. Huson. OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics, 23:1573-1579, 2007. (Pubitemid 47244446)
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 1573-1579
-
-
Richter, D.C.1
Schuster, S.C.2
Huson, D.H.3
-
23
-
-
68549115571
-
Reordering contigs of draft genomes using the Mauve aligner
-
A. I. Rissman, B. Mau, B. S. Biehl, A. E. Darling, J. D. Glasner, and N. T. Perna. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics, 25:2071-2073, 2009.
-
(2009)
Bioinformatics
, vol.25
, pp. 2071-2073
-
-
Rissman, A.I.1
Mau, B.2
Biehl, B.S.3
Darling, A.E.4
Glasner, J.D.5
Perna, N.T.6
-
24
-
-
60849119540
-
Inversion-based genomic signatures
-
K. Swenson and B. Moret. Inversion-based genomic signatures. BMC Bioinformatics, 10(Suppl. 1):S7, 2009.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 1
-
-
Swenson, K.1
Moret, B.2
-
25
-
-
33646882185
-
Refinement of optical map assemblies
-
DOI 10.1093/bioinformatics/btl063
-
A. Valouev, Y. Zhang, D. C. Schwartz, and M. S. Waterman. Refinement of optical map assemblies. Bioinformatics, 22:1217-1224, 2006. (Pubitemid 43779014)
-
(2006)
Bioinformatics
, vol.22
, Issue.10
, pp. 1217-1224
-
-
Valouev, A.1
Zhang, Y.2
Schwartz, D.C.3
Waterman, M.S.4
-
26
-
-
23144442407
-
Projector 2: Contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
-
DOI 10.1093/nar/gki356
-
S. A. van Hijum, A. L. Zomer, O. P. Kuipers, and J. Kok. Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res., 33:W560-566, 2005. (Pubitemid 44529984)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISSUE
-
-
Van Hijum, S.A.F.T.1
Zomer, A.L.2
Kuipers, O.P.3
Kok, J.4
-
27
-
-
33744779610
-
Physical map-assisted whole-genome shotgun sequence assemblies
-
DOI 10.1101/gr.5090606
-
R. L. Warren, D. Varabei, D. Platt, X. Huang, D. Messina, S. P. Yang, J. W. Kronstad, M. Krzywinski, W. C. Warren, J. W. Wallis, L. W. Hillier, A. T. Chinwalla, J. E. Schein, A. S. Siddiqui, M. A. Marra, R. K. Wilson, and S. J. Jones. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res., 16:768-775, 2006. (Pubitemid 43830697)
-
(2006)
Genome Research
, vol.16
, Issue.6
, pp. 768-775
-
-
Warren, R.L.1
Varabei, D.2
Platt, D.3
Huang, X.4
Messina, D.5
Yang, S.-P.6
Kronstad, J.W.7
Krzywinski, M.8
Warren, W.C.9
Wallis, J.W.10
Hillier, L.W.11
Chinwalla, A.T.12
Schein, J.E.13
Siddiqui, A.S.14
Marra, M.A.15
Wilson, R.K.16
Jones, S.J.M.17
|