-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
38549164691
-
GenBank
-
Benson, D., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. 2008. GenBank. Nucleic Acids Res. 36:D25-D30.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D25-D30
-
-
Benson, D.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
3
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., and Schneider, M. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
4
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10:421.
-
(2009)
BMC Bioinformatics
, 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
-
5
-
-
38549170427
-
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
-
Cochrane, G., Akhtar, R., Aldebert, P., Althorpe, N., Baldwin, A., Bates, K., Bhattacharyya, S., Bonfield, J., and Bower, L. 2007. Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 36:D5-D12.
-
(2007)
Nucleic Acids Res.
, vol.36
, pp. D5-D12
-
-
Cochrane, G.1
Akhtar, R.2
Aldebert, P.3
Althorpe, N.4
Baldwin, A.5
Bates, K.6
Bhattacharyya, S.7
Bonfield, J.8
Bower, L.9
-
6
-
-
33846040145
-
FlyBase: Genomes by the dozen
-
Crosby, M.A., Goodman, J.L., Strelets, V.B., Zhang, P., Gelbart, W.M., and FlyBase Consortium. 2007. FlyBase: Genomes by the dozen. Nucleic Acids Res. 35:D486-D491.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D486-D491
-
-
Crosby, M.A.1
Goodman, J.L.2
Strelets, V.B.3
Zhang, P.4
Gelbart, W.M.5
FlyBase, Consortium.6
-
7
-
-
0001433809
-
Method for determination of the amino acid sequence in peptides
-
Edman, P., Högfeldt, E., Sillén, L.G., and Kinell, P. 1950. Method for determination of the amino acid sequence in peptides. Acta Chem. Scand. 4:283-293.
-
(1950)
Acta Chem. Scand.
, vol.4
, pp. 283-293
-
-
Edman, P.1
Högfeldt, E.2
Sillén, L.G.3
Kinell, P.4
-
8
-
-
78651289449
-
Ensembl 2011
-
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H.S., Rios, D., Ritchie, G.R., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y.A., Trevanion, S., Vandrovcova, J., Vilella, A.J., White, S., Wilder, S.P., Zadissa, A., Zamora, J., Aken, B.L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, X.M., Herrero, J., Hubbard, T.J., Parker, A., Proctor, G., Vogel, J., and Searle, S.M. 2011. Ensembl 2011. Nucleic Acids Res. 39:D800-D806.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D800-D806
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Chen, Y.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
Gordon, L.11
Hendrix, M.12
Hourlier, T.13
Johnson, N.14
Kähäri, A.15
Keefe, D.16
Keenan, S.17
Kinsella, R.18
Kokocinski, F.19
Kulesha, E.20
Larsson, P.21
Longden, I.22
McLaren, W.23
Overduin, B.24
Pritchard, B.25
Riat, H.S.26
Rios, D.27
Ritchie, G.R.28
Ruffier, M.29
Schuster, M.30
Sobral, D.31
Spudich, G.32
Tang, Y.A.33
Trevanion, S.34
Vandrovcova, J.35
Vilella, A.J.36
White, S.37
Wilder, S.P.38
Zadissa, A.39
Zamora, J.40
Aken, B.L.41
Birney, E.42
Cunningham, F.43
Dunham, I.44
Durbin, R.45
Fernández-Suarez, X.M.46
Herrero, J.47
Hubbard, T.J.48
Parker, A.49
Proctor, G.50
Vogel, J.51
Searle, S.M.52
more..
-
9
-
-
0000354379
-
Structure of tobacco mosaic virus: Location of the ribonucleic acid in the tobacco mosaic virus particle
-
Franklin, R.E. 1956. Structure of tobacco mosaic virus: Location of the ribonucleic acid in the tobacco mosaic virus particle. Nature 177:928-930 Gonzalez, M.W. and Pearson, W.R. 2010. Homologous over-extension: A challenge for iterative similarity searches. Nucleic Acids Res. 38:2177-2189.
-
(1956)
Nature
, vol.177
, pp. 928-930
-
-
Franklin, R.E.1
-
10
-
-
77952296596
-
Homologous over-extension: A challenge for iterative similarity searches
-
Gonzalez, M.W. and Pearson, W.R. 2010. Homologous over-extension: A challenge for iterative similarity searches. Nucleic Acids Res. 38:2177-2189
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2177-2189
-
-
Gonzalez, M.W.1
Pearson, W.R.2
-
11
-
-
77954296666
-
A new bioinformatics analysis tools framework at EMBL-EBI
-
Goujon, M., McWilliam, H., Li, W., Valentin, F., Squizzato, S., Paern, J., and Lopez, R. 2010. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 38:W695-W699.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W695-W699
-
-
Goujon, M.1
McWilliam, H.2
Li, W.3
Valentin, F.4
Squizzato, S.5
Paern, J.6
Lopez, R.7
-
12
-
-
75549084124
-
WormBase: A comprehensive resource for nematode research
-
Harris, T.W., Antoshechkin, I., Bieri, T., Blasiar, D., Chan, J., Chen, W.J., De La Cruz, N., Davis, P., Duesbury, M., Fang, R., Fernandes, J., Han, M., Kishore, R., Lee, R., Müller, H.M., Nakamura, C., Ozersky, P., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G, Schwarz, E.M., Tuli, M.A., Van Auken, K., Wang, D., Wang, X., Williams, G., Yook, K., Durbin, R., Stein, L.D., Spieth, J., and Sternberg, P.W. 2009. WormBase: A comprehensive resource for nematode research. Nucleic Acids Res. 38:D463-D467.
-
(2009)
Nucleic Acids Res.
, vol.38
, pp. D463-D467
-
-
Harris, T.W.1
Antoshechkin, I.2
Bieri, T.3
Blasiar, D.4
Chan, J.5
Chen, W.J.6
De La Cruz, N.7
Davis, P.8
Duesbury, M.9
Fang, R.10
Fernandes, J.11
Han, M.12
Kishore, R.13
Lee, R.14
Müller, H.M.15
Nakamura, C.16
Ozersky, P.17
Petcherski, A.18
Rangarajan, A.19
Rogers, A.20
Schindelman, G.21
Schwarz, E.M.22
Tuli, M.A.23
Van Auken, K.24
Wang, D.25
Wang, X.26
Williams, G.27
Yook, K.28
Durbin, R.29
Stein, L.D.30
Spieth, J.31
Sternberg, P.W.32
more..
-
14
-
-
33644898528
-
Automated protein identification by tandem mass spectrometry: Issues and strategies
-
Automated protein identification by tandem mass spectrometry: Issues and strategies. Mass Spectrom. Rev. 25:235-254.
-
Mass Spectrom. Rev.
, vol.25
, pp. 235-254
-
-
-
15
-
-
84899518211
-
Inter- ProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A.F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S.Y., Lopez, R., and Hunter, S. 2014. Inter- ProScan 5: Genome-scale protein function classification. Bioinformatics 30:1236-1240.
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.Y.3
Fraser, M.4
Li, W.5
McAnulla, C.6
McWilliam, H.7
Maslen, J.8
Mitchell, A.9
Nuka, G.10
Pesseat, S.11
Quinn, A.F.12
Sangrador-Vegas, A.13
Scheremetjew, M.14
Yong, S.Y.15
Lopez, R.16
Hunter, S.17
-
16
-
-
84862234514
-
Ensembl genomes: An integrative resource for genome-scale data from non-vertebrate species
-
Kersey, P.J., Staines, D.M., Lawson, D., Kulesha, E., Derwent, P., Humphrey, J.C., Hughes, D.S.T., Keenan, S., Kerhornou, A., Koscielny, G., Langridge, N., McDowall, M.D., Megy, K., Maheswari, U., Nuhn, M., Paulini, M., Pedro, H., Toneva, I., Wilson, D., Yates, A., and Birney, E. 2011. Ensembl genomes: An integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 40: D91-D97.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. D91-D97
-
-
Kersey, P.J.1
Staines, D.M.2
Lawson, D.3
Kulesha, E.4
Derwent, P.5
Humphrey, J.C.6
Hughes, D.S.T.7
Keenan, S.8
Kerhornou, A.9
Koscielny, G.10
Langridge, N.11
McDowall, M.D.12
Megy, K.13
Maheswari, U.14
Nuhn, M.15
Paulini, M.16
Pedro, H.17
Toneva, I.18
Wilson, D.19
Yates, A.20
Birney, E.21
more..
-
17
-
-
84949306210
-
-
Li, W., McWilliam, H., Goujon, M., Cowley, A., Lopez, R., and Pearson, W.R. 2012.
-
(2012)
-
-
Li, W.1
McWilliam, H.2
Goujon, M.3
Cowley, A.4
Lopez, R.5
Pearson, W.R.6
-
18
-
-
84863531160
-
PSI-Search: Iterative HOE-reduced profile SSEARCH searching
-
PSI-Search: Iterative HOE-reduced profile SSEARCH searching. Bioinformatics 28:1650-1651.
-
Bioinformatics
, vol.28
, pp. 1650-1651
-
-
-
19
-
-
4143095783
-
Public services from the European Bioinformatics Institute
-
Lopez, R., Duggan, K., Harte, N., and Kibria, A. 2003 Public services from the European Bioinformatics Institute. Brief. Bioinform. 4:332-340.
-
(2003)
Brief. Bioinform.
, vol.4
, pp. 332-340
-
-
Lopez, R.1
Duggan, K.2
Harte, N.3
Kibria, A.4
-
20
-
-
34347394165
-
Towards a comprehensive structural coverage of completed genomes: A structural genomics viewpoint
-
Marsden, R.L., Lewis, T.A., and Orengo, C.A. 2007. Towards a comprehensive structural coverage of completed genomes: A structural genomics viewpoint. BMC Bioinformatics 8:86.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 86
-
-
Marsden, R.L.1
Lewis, T.A.2
Orengo, C.A.3
-
21
-
-
67849111574
-
Web services at the European Bioinformatics Institute-2009
-
McWilliam, H., Valentin, F., Goujon, M., Li, W., Narayanasamy, M., Martin, J., Miyar, T., and Lopez, R. 2009. Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res. 37:W6-W10.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W6-W10
-
-
McWilliam, H.1
Valentin, F.2
Goujon, M.3
Li, W.4
Narayanasamy, M.5
Martin, J.6
Miyar, T.7
Lopez, R.8
-
22
-
-
84883577718
-
Analysis tool web services from the EMBL-EBI
-
McWilliam, H., Li, W., Uludagi, M., Squizzato, S., Park, Y.M., Buso, N., Cowley, A.P., and Lopez, R. 2013. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 41:W597-W600.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W597-W600
-
-
McWilliam, H.1
Li, W.2
Uludagi, M.3
Squizzato, S.4
Park, Y.M.5
Buso, N.6
Cowley, A.P.7
Lopez, R.8
-
23
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W.R. 1991. Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11:635-650.
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
-
24
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85:2444-2448.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
25
-
-
58249138817
-
Generations of sequencing technologies
-
Pettersson, E., Lundeberg, J., and Ahmadian, A. 2009. Generations of sequencing technologies. Genomics 93:105-111.
-
(2009)
Genomics
, vol.93
, pp. 105-111
-
-
Pettersson, E.1
Lundeberg, J.2
Ahmadian, A.3
-
26
-
-
0017021326
-
Restriction endonucleases. CRC Crit
-
Roberts, R.J. 1976. Restriction endonucleases. CRC Crit. Rev. Biochem. 4:123-164.
-
(1976)
Rev. Biochem.
, vol.4
, pp. 123-164
-
-
Roberts, R.J.1
-
27
-
-
0016800090
-
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
-
Sanger, F. and Coulson, A.R. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94:441-448.
-
(1975)
J. Mol. Biol.
, vol.94
, pp. 441-448
-
-
Sanger, F.1
Coulson, A.R.2
-
28
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J.D., and Higgins, D.G. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Soding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
29
-
-
0036081078
-
DNA Data Bank of Japan (DDBJ) for genome scale research in life science
-
Tateno, Y., Imanishi, T., Miyazaki, S., Fukami- Kobayashi, K., Saitou, N., Sugawara, H., and Gojobori, T. 2002. DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res. 30:27-30.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 27-30
-
-
Tateno, Y.1
Imanishi, T.2
Miyazaki, S.3
Fukami-Kobayashi, K.4
Saitou, N.5
Sugawara, H.6
Gojobori, T.7
-
30
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
UniProt Consortium. 2010. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39:D214-D219.
-
(2010)
Nucleic Acids Res.
, vol.39
, pp. D214-D219
-
-
-
31
-
-
77954245304
-
Fast and efficient searching of biological data resources-using EB-eye
-
Valentin, F., Squizzato, S., Goujon, M., McWilliam, H., Paern, J., and Lopez, R. 2010. Fast and efficient searching of biological data resources-using EB-eye. Brief. Bioinform. 11:375-384.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 375-384
-
-
Valentin, F.1
Squizzato, S.2
Goujon, M.3
McWilliam, H.4
Paern, J.5
Lopez, R.6
-
32
-
-
65449188232
-
Jalview Version 2:Amultiple sequence alignment editor and analysis workbench
-
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., and Barton, G.J. 2009. Jalview Version 2:Amultiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189-1191.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin D.M.A Clamp, M.3
Barton, G.J.4
-
33
-
-
16644373279
-
Update on genome completion and annotations: Protein Information Resource
-
Wu, C. and Nebert, D.W. 2004. Update on genome completion and annotations: Protein Information Resource. Hum. Genomics 1:229-233.
-
(2004)
Hum. Genomics
, vol.1
, pp. 229-233
-
-
Wu, C.1
Nebert, D.W.2
|