-
1
-
-
80955159932
-
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
-
10.1089/cmb.2011.0170, 3216105, 21929371
-
Gao S, Sung WK, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011, 18(11):1681-1691. 10.1089/cmb.2011.0170, 3216105, 21929371.
-
(2011)
J Comput Biol
, vol.18
, Issue.11
, pp. 1681-1691
-
-
Gao, S.1
Sung, W.K.2
Nagarajan, N.3
-
2
-
-
33744779610
-
Physical map-assisted whole-genome shotgun sequence assemblies
-
10.1101/gr.5090606, 1473187, 16741162
-
Warren RL, Varabei D, Platt D, Huang X, et al. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res 2006, 16:768-775. 10.1101/gr.5090606, 1473187, 16741162.
-
(2006)
Genome Res
, vol.16
, pp. 768-775
-
-
Warren, R.L.1
Varabei, D.2
Platt, D.3
Huang, X.4
-
3
-
-
43349084767
-
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
-
10.1093/bioinformatics/btn102, 2373919, 18356192
-
Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 2008, 24:1229-1235. 10.1093/bioinformatics/btn102, 2373919, 18356192.
-
(2008)
Bioinformatics
, vol.24
, pp. 1229-1235
-
-
Nagarajan, N.1
Read, T.D.2
Pop, M.3
-
4
-
-
33646882185
-
Refinement of optical map assemblies
-
10.1093/bioinformatics/btl063, 16500933
-
Valouev A, Zhang Y, Schwartz DC, Waterman MS. Refinement of optical map assemblies. Bioinformatics 2006, 22:1217-1224. 10.1093/bioinformatics/btl063, 16500933.
-
(2006)
Bioinformatics
, vol.22
, pp. 1217-1224
-
-
Valouev, A.1
Zhang, Y.2
Schwartz, D.C.3
Waterman, M.S.4
-
5
-
-
67650735586
-
ABACAS: algorithm-based automatic contiguation of assembled sequences
-
10.1093/bioinformatics/btp347, 2712343, 19497936
-
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 2009, 25:1968-1969. 10.1093/bioinformatics/btp347, 2712343, 19497936.
-
(2009)
Bioinformatics
, vol.25
, pp. 1968-1969
-
-
Assefa, S.1
Keane, T.M.2
Otto, T.D.3
Newbold, C.4
Berriman, M.5
-
6
-
-
77953019477
-
Scaffold filling, contig fusion and comparative gene order inference
-
Munoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D. Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinf 2010, 11:304.
-
(2010)
BMC Bioinf
, vol.11
, pp. 304
-
-
Munoz, A.1
Zheng, C.2
Zhu, Q.3
Albert, V.A.4
Rounsley, S.5
Sankoff, D.6
-
7
-
-
68549115571
-
Reordering contigs of draft genomes using the Mauve aligner
-
10.1093/bioinformatics/btp356, 2723005, 19515959
-
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 2009, 25:2071-2073. 10.1093/bioinformatics/btp356, 2723005, 19515959.
-
(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
-
8
-
-
34547852218
-
OSLay: optimal syntenic layout of unfinished assemblies
-
10.1093/bioinformatics/btm153, 17463020
-
Richter DC, Schuster SC, Huson DH. OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics 2007, 23:1573-1579. 10.1093/bioinformatics/btm153, 17463020.
-
(2007)
Bioinformatics
, vol.23
, pp. 1573-1579
-
-
Richter, D.C.1
Schuster, S.C.2
Huson, D.H.3
-
9
-
-
23144442407
-
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
-
10.1093/nar/gki356, 1160117, 15980536
-
van H, Zomer AL, Kuipers OP, Kok J. Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 2005, 33:W560-566. 10.1093/nar/gki356, 1160117, 15980536.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
van, H.1
Zomer, A.L.2
Kuipers, O.P.3
Kok, J.4
-
10
-
-
77949515650
-
R2cat: synteny plots and comparative assembly
-
10.1093/bioinformatics/btp690, 2820676, 20015948
-
Husemann P, Stoye J. r2cat: synteny plots and comparative assembly. Bioinformatics 2010, 26:570-571. 10.1093/bioinformatics/btp690, 2820676, 20015948.
-
(2010)
Bioinformatics
, vol.26
, pp. 570-571
-
-
Husemann, P.1
Stoye, J.2
-
11
-
-
70249111111
-
PGA4genomics for comparative genome assembly based on genetic algorithm optimization
-
10.1016/j.ygeno.2009.06.006, 19573591
-
Zhao F, Hou H, Bao Q, Wu J. PGA4genomics for comparative genome assembly based on genetic algorithm optimization. Genomics 2009, 94:284-286. 10.1016/j.ygeno.2009.06.006, 19573591.
-
(2009)
Genomics
, vol.94
, pp. 284-286
-
-
Zhao, F.1
Hou, H.2
Bao, Q.3
Wu, J.4
-
12
-
-
79959240236
-
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes
-
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 2011, 6(11).
-
(2011)
Source Code Biol Med
, vol.6
, Issue.11
-
-
Galardini, M.1
Biondi, E.G.2
Bazzicalupo, M.3
Mengoni, A.4
-
13
-
-
48249144818
-
Dynamics of genome rearrangement in bacterial populations
-
10.1371/journal.pgen.1000128, 2483231, 18650965
-
Darling AE, Miklós I, Ragan MA. Dynamics of genome rearrangement in bacterial populations. PLoS Genet 2008, 4(7):e1000128. 10.1371/journal.pgen.1000128, 2483231, 18650965.
-
(2008)
PLoS Genet
, vol.4
, Issue.7
-
-
Darling, A.E.1
Miklós, I.2
Ragan, M.A.3
-
14
-
-
0034568798
-
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
-
Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000, 1(6):research0011.1-0011.9.
-
(2000)
Genome Biol
, vol.1
, Issue.6
-
-
Eisen, J.A.1
Heidelberg, J.F.2
White, O.3
Salzberg, S.L.4
-
15
-
-
3543051830
-
Mauve: multiple alignment of conserved genomic sequence with rearrangements
-
10.1101/gr.2289704, 442156, 15231754
-
Darling AE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403. 10.1101/gr.2289704, 442156, 15231754.
-
(2004)
Genome Res
, vol.14
, pp. 1394-1403
-
-
Darling, A.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
16
-
-
0347724102
-
GRIL: genome rearrangement and inversion locator
-
10.1093/bioinformatics/btg378, 14693819
-
Darling AE, Mau B, Blattner FR, Perna NT. GRIL: genome rearrangement and inversion locator. Bioinformatics 2004, 20:122-124. 10.1093/bioinformatics/btg378, 14693819.
-
(2004)
Bioinformatics
, vol.20
, pp. 122-124
-
-
Darling, A.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
17
-
-
60849119540
-
Inversion-based genomic signatures
-
2648787, 19208174
-
Swenson KM, Moret BM. Inversion-based genomic signatures. BMC Bioinformatics 2009, 10 Suppl 1:S7. 2648787, 19208174.
-
(2009)
BMC Bioinformatics
, Issue.10 SUPPL. 1
-
-
Swenson, K.M.1
Moret, B.M.2
-
18
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
10.1186/gb-2004-5-2-r12, 395750, 14759262
-
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5(2):R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
-
(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
-
19
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
187518, 11932250
-
Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul S, Madden T, Schäffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schäffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
21
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinf 2009, 10:421.
-
(2009)
BMC Bioinf
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
23
-
-
58149527706
-
A genomic distance based on MUM indicates discontinuity between most bacterial species and genera
-
10.1128/JB.01202-08, 2612450, 18978054
-
Deloger M, El K, Petit MA. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 2009, 191:91-99. 10.1128/JB.01202-08, 2612450, 18978054.
-
(2009)
J Bacteriol
, vol.191
, pp. 91-99
-
-
Deloger, M.1
El, K.2
Petit, M.A.3
-
24
-
-
84858968503
-
Using Inversion Signatures to Generate Draft Genome Sequence Scaffolds
-
,
-
Dias Z, Dias U, Setubal JC. Using Inversion Signatures to Generate Draft Genome Sequence Scaffolds. Proceedings of the 2nd ACM International Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011) 2011, 39-48. , .
-
(2011)
Proceedings of the 2nd ACM International Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011)
, pp. 39-48
-
-
Dias, Z.1
Dias, U.2
Setubal, J.C.3
-
25
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 2000, 132:365-386.
-
(2000)
Methods in Molecular Biology
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
|