-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215:403-10.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
5
-
-
25444486385
-
Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system
-
Diener SE, Houfek TD, Kalat SE, et al. Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system. BMC Bioinformatics 2005;6:1-5.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 1-5
-
-
Diener, S.E.1
Houfek, T.D.2
Kalat, S.E.3
-
6
-
-
0034854994
-
Multi-query sequence BLAST output examination with MuSeqBox
-
Xing L, Brendel V. Multi-query sequence BLAST output examination with MuSeqBox. Bioinformatics 2001;17:744-5.
-
(2001)
Bioinformatics
, vol.17
, pp. 744-745
-
-
Xing, L.1
Brendel, V.2
-
8
-
-
52249115174
-
Batch Blast Extractor: an automated blastx parser application
-
Pirooznia M, Perkins EJ, Deng Y. Batch Blast Extractor: an automated blastx parser application. BMC Genomics 2008;9:1-5.
-
(2008)
BMC Genomics
, vol.9
, pp. 1-5
-
-
Pirooznia, M.1
Perkins, E.J.2
Deng, Y.3
-
9
-
-
4444294287
-
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
-
Suyama M, Torrents D, Bork P. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics 2004;20:1968-70.
-
(2004)
Bioinformatics
, vol.20
, pp. 1968-1970
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
10
-
-
24644493288
-
BlastXtract-a new way of exploring translated searches
-
Claesson MJ, van Sinderen D. BlastXtract-a new way of exploring translated searches. Bioinformatics 2005;21:3667-8.
-
(2005)
Bioinformatics
, vol.21
, pp. 3667-3668
-
-
Claesson, M.J.1
van Sinderen, D.2
-
12
-
-
62649147821
-
Sequence context-specific profiles for homology searching
-
Biegert A, Söding J. Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA 2009;106:3770-5.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 3770-3775
-
-
Biegert, A.1
Söding, J.2
-
13
-
-
84859739224
-
Domain enhanced lookup time accelerated BLAST
-
Boratyn G, Schaffer A, Agarwala R, et al. Domain enhanced lookup time accelerated BLAST. Biol Direct 2012;7:1-14.
-
(2012)
Biol Direct
, vol.7
, pp. 1-14
-
-
Boratyn, G.1
Schaffer, A.2
Agarwala, R.3
-
14
-
-
0028276887
-
A workbench for large-scale sequence homology analysis
-
Sonnhammer EL, Durbin R. A workbench for large-scale sequence homology analysis. Comp Appl Biosci 1994;10:301-7.
-
(1994)
Comp Appl Biosci
, vol.10
, pp. 301-307
-
-
Sonnhammer, E.L.1
Durbin, R.2
-
16
-
-
0030876345
-
Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT
-
Durand P, Canard L, Mornon JP. Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT. Comp Appl Biosci 1997;13:407-13.
-
(1997)
Comp Appl Biosci
, vol.13
, pp. 407-413
-
-
Durand, P.1
Canard, L.2
Mornon, J.P.3
-
17
-
-
33847113939
-
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
-
He J, Dai X, Zhao X. PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics 2007;8:1-10.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 1-10
-
-
He, J.1
Dai, X.2
Zhao, X.3
-
18
-
-
84928242653
-
Massive data visualization: a survey
-
In: Moller T, Hamann B, Russell RD (eds), Berlin: Springer Verlag
-
Joy KI. Massive data visualization: a survey. In: Moller T, Hamann B, Russell RD (eds). Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration. Berlin: Springer Verlag, 2009;285-302.
-
(2009)
Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration
, pp. 285-302
-
-
Joy, K.I.1
-
19
-
-
62549119131
-
NOBLAST and JAMBLAST: new options for BLAST and a Java Application Manager for BLAST results
-
Lagnel J, Tsigenopoulos CS, Iliopoulos I. NOBLAST and JAMBLAST: new options for BLAST and a Java Application Manager for BLAST results. Bioinformatics 2009;25:824-6.
-
(2009)
Bioinformatics
, vol.25
, pp. 824-826
-
-
Lagnel, J.1
Tsigenopoulos, C.S.2
Iliopoulos, I.3
-
20
-
-
24644503098
-
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa A, Götz S, García-Gómez JM, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21:3674-6.
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
Götz, S.2
García-Gómez, J.M.3
-
21
-
-
79961109150
-
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
-
Nabil-Fareed A, Nicola P, Nouri BZ, et al. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:1-10.
-
(2011)
BMC Genomics
, vol.12
, pp. 1-10
-
-
Nabil-fareed, A.1
Nicola, P.2
Nouri, B.Z.3
-
22
-
-
84872840904
-
An eQTL biological data visualization challenge and approaches from the visualization community
-
Bartlett CW, Cheong SY, Hou L, et al. An eQTL biological data visualization challenge and approaches from the visualization community. BMC Bioinformatics 2012;13:1-16.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-16
-
-
Bartlett, C.W.1
Cheong, S.Y.2
Hou, L.3
-
23
-
-
1842845736
-
The Bio* toolkits - a brief overview
-
Mangalam H. The Bio* toolkits - a brief overview. Brief Bioinform 2002;3:296-302.
-
(2002)
Brief Bioinform
, vol.3
, pp. 296-302
-
-
Mangalam, H.1
-
24
-
-
0034139835
-
Database searching with DNA and protein sequences: an introduction
-
Sansom C. Database searching with DNA and protein sequences: an introduction. Brief Bioinform 2000;1:22-32.
-
(2000)
Brief Bioinform
, vol.1
, pp. 22-32
-
-
Sansom, C.1
-
25
-
-
84904721221
-
BlastViewer
-
Korilog, Questembert, France, 18 January, date last accessed
-
Korilog, Questembert, France. BlastViewer. http://www.korilog.com/index.php/BlastViewer.html (18 January 2013, date last accessed).
-
(2013)
-
-
-
26
-
-
84904731422
-
BLASTGrabber
-
18 January, date last accessed
-
Neumann R, Kumar S, Haverkamp THA, et al. BLASTGrabber. http://www.mn.uio.no/ibv/english/people/aca/kamran/software/blastgrabber/ (18 January 2013, date last accessed).
-
(2013)
-
-
Neumann, R.1
Kumar, S.2
Haverkamp, T.H.A.3
-
27
-
-
84904751708
-
BlastStation-Free
-
TMSoftware, Arcadia, USA., 18 January, date last accessed
-
TMSoftware, Arcadia, USA. BlastStation-Free. http://www.blaststation.com/ (18 January 2013, date last accessed).
-
(2013)
-
-
-
28
-
-
84863507534
-
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data
-
Kearse M, Moir R, Wilson A, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647-9.
-
(2012)
Bioinformatics
, vol.28
, pp. 1647-1649
-
-
Kearse, M.1
Moir, R.2
Wilson, A.3
-
29
-
-
33645033905
-
BioParser: a tool for processing of sequence similarity analysis reports
-
Catanho M, Mascarenhas D, Degrave W, et al. BioParser: a tool for processing of sequence similarity analysis reports. Appl Bioinformatics 2006;5:49-53.
-
(2006)
Appl Bioinformatics
, vol.5
, pp. 49-53
-
-
Catanho, M.1
Mascarenhas, D.2
Degrave, W.3
-
30
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
Huson DH, Auch AF, Qi J, et al. MEGAN analysis of metagenomic data. Genome Res 2007;17:377-86.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
-
31
-
-
77957793364
-
Circoletto: visualizing sequence similarity with Circos
-
Darzentas N. Circoletto: visualizing sequence similarity with Circos. Bioinformatics 2010;26:2620-1.
-
(2010)
Bioinformatics
, vol.26
, pp. 2620-2621
-
-
Darzentas, N.1
-
32
-
-
76749119387
-
BLASTEXPLORER helps you building datasets for phylogenetic analysis
-
Dereeper A, Audic S, Claverie J-M, et al. BLASTEXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 2010;10:1-6.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 1-6
-
-
Dereeper, A.1
Audic, S.2
Claverie, J.-M.3
-
33
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000;25:25-9.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
34
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012;40:D109-14.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
-
35
-
-
84904739583
-
WU-BLAST
-
18 January, date last accessed
-
Gish W. WU-BLAST. http://blast.wustl.edu/ (18 January 2013, date last accessed).
-
(2013)
-
-
Gish, W.1
-
36
-
-
80053212413
-
Ortholog identification in the presence of domain architecture rearrangement
-
Sjölander K, Datta RS, Shen Y, et al. Ortholog identification in the presence of domain architecture rearrangement. Brief Bioinform 2011;12:413-22.
-
(2011)
Brief Bioinform
, vol.12
, pp. 413-422
-
-
Sjölander, K.1
Datta, R.S.2
Shen, Y.3
-
37
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin EV. Orthologs, paralogs, and evolutionary genomics. Ann Rev Genet 2005;39:309-38.
-
(2005)
Ann Rev Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
38
-
-
60049093585
-
ASTD: the Alternative Splicing and Transcript Diversity database
-
Koscielny G, Le Texier V, Gopalakrishnan C, et al. ASTD: the Alternative Splicing and Transcript Diversity database. Genomics 2009;93:213-20.
-
(2009)
Genomics
, vol.93
, pp. 213-220
-
-
Koscielny, G.1
Le Texier, V.2
Gopalakrishnan, C.3
-
39
-
-
84862245279
-
Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction
-
Ye J, Coulouris G, Zaretskaya I, et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 2012;13:1-11.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 1-11
-
-
Ye, J.1
Coulouris, G.2
Zaretskaya, I.3
-
40
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell M, Ence D. A beginner's guide to eukaryotic genome annotation. Nat Rev Genet 2012;13:329-42.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
41
-
-
84871125786
-
Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data
-
Frisli T, Haverkamp THA, Jakobsen KS, et al. Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data. J Appl Microbiol 2012;114:141-51.
-
(2012)
J Appl Microbiol
, vol.114
, pp. 141-151
-
-
Frisli, T.1
Haverkamp, T.H.A.2
Jakobsen, K.S.3
-
42
-
-
84856566415
-
Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments
-
Ma Y, Paulsen IT, Palenik B. Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environ Microbiol 2012;14:453-66.
-
(2012)
Environ Microbiol
, vol.14
, pp. 453-466
-
-
Ma, Y.1
Paulsen, I.T.2
Palenik, B.3
-
43
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 2011;6:1-11.
-
(2011)
PLoS One
, vol.6
, pp. 1-11
-
-
Schmieder, R.1
Edwards, R.2
|