Citations & References¶
Note
It is important that you cite T-Coffee when you use it. Citing us is (almost) like giving us money: it helps us convincing our institutions that what we do is useful and that they should keep paying our salaries and deliver donuts to our offices from time to time (Not that they ever did it, but it would be nice anyway). Cite the approriate web server if you use one, otherwise, cite the original paper from 2000 (By the way…NOOO, it was never named ‘T-Coffee 2000’).
Comparative Genomics & Biology¶
Erb, I., Notredame, C. How should we measure proportionality on relative gene expression data? Theory Biosci., 135(1-2):21-36 (2016), PMID26762323
Catuara-Solarz, S., Espinosa-Carrasco, J., Erb, I., Langohr, K., Gonzalez, J.R., Notredame, C., Dierssen, M. Combined treatment with environmental enrichment and (-)-epigallocatchin-3-gallate ameliorates learning deficits and hippocampal alterations in a mouse model of Down syndrome. eNeuro., 3(5)(2015) pii:ENEURO.0103, PMID:27844057
Di Tommaso, P., Palumbo, E., Chatzou, M., Prieto, P.,Heuer, M.L., Notredame, C. The impact of Docker containers on ther performance of genomic pipelines. PeerJ., 3:e1273 (2015), PMID:26421241
Catuara-Solarz, S., Espinosa-Carrasco, J., Erb, I., Langohr, K., Notredame, C., Gonzalez, J.R., Dierssen, M. Principal component analysis of the effects of environmental enrichment and (-)-epigallocatchin-3-gallate on age-associated learning deficits in a mouse model of Down syndrome. Front Behav. Neurosci., 9:330 (2015), PMID:26696850
Earl, D., Nguyen, N., Hickey, G., Harris, R.S., Fitzgerald, S., Beal, K. Seledtsov, I., Raney, B.J., Clawson, H., Kim, J., Kemena, C., Chang, J.-M., Erb, I., Poliakov, A., Hou, M., Herrero, J., Kent, W.J., Solovyev, V., Darling, A.E., Ma, J., Notredame, C., Brudno, M., Dubchak, I., Haussler, D., Paten, B. Alignathon: a competitive assessment of whole-geome alignment methods. Genome Res., 24(12):2077-2089 (2014), PMID:25273068
The mouse ENCODE Consortium. A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527):355-364 (2014), PMID:25409824
Bussotti, G., Notredame, C., Enright, A.J. Detecting and comparing non-coding RNAs in the high-throughput era. Int. J. Mol. Sci., 14(8):15423-15458 (2013), PMID:23887659
Chang, J.-M., Taly, J.-F., Erb, I., Sung, T.Y., Hsu, W.L. Tang, C.Y., Notredame, C., Su, E.C. Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations. PLoS One, 8(10):e75542 (2013), PMID:24146760
Magis, C., van der Sloot, A.M., Serrano, L., Notredame, C. An improved understanding of TNFL/TNFR interactions using structure-based classifications. Trends Biochem. Sci., 37(9):353-363 (2012), PMID:22789664
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Brown, J.B., Lipovich, L., Gonzalez, J.M., Davis, C.A., Shiekhattar, R., Gingeras, T.R., Hubbard, T.J., Notredame, C., Harrow, J., Guigó, R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution and expression. Genome Res., 22(9):1775-1789 (2012), PMID:22955988
Breen, M.S., Kemena, C., Vlasov, P.K., Notredame, C., Kondrashov, F.A. Epistasis as the primary factor in molecular evolution. Nature, 490(7421), 535-538 (2012), PMID:23064225
Bussotti, G., Raineri, E., Erb, I., Zytnicki, M., Wilm, A., Beaudoing, E., Bucher, P., Notredame, C. BlastR-fast and accurate database searches for non-coding RNAs. Nucleic Acids Res., 39(16):6886-6895 (2011), PMID:21624887
Lin, H.N., Notredame, C., Chang, J.-M., Sung, T.Y., Hsu, W.L. Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words. PLoS One, 6(12):e27872, (2011), PMID:22163274
Ørom, U.A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., Guigo, R., Shiekhattar, R. Long noncoding RNAs with enhancer-like function in human cells. Cell, 143(1):46-58 (2010), PMID:20887892
Coll, O., Villalba, A., Bussotti, G., Notredame, C., Gebauer, F. A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis. Genes Dev., 24(2):129-134 (2010), PMID:20080951
Rausch, T., Emde, A.K., Weese, D., Döring, A., Notredame, C., Reinert, K. Segment-based multiple sequence alignment. Bioinformatics, 24(16):i187-i192 (2008), PMID:18689823
Dietmann, S:, Park, J., Notredame, C., Heger, A., Lappe, M., Holm, L. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res., 29(1):55-57 (2001), PMID:11125048
T-Coffee Alignment Methods¶
Kemena, C., Bussotti, G., Capriotti, E., Marti-Renom, M.A., Noredame, C. Using tertiary structure for computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinformatics, 29(9):1112-1119 (2013), PMID:234490094
Erb, I., González-Vallinas, J.R., Bussotti, G., Blanco, E., Eyras, E., Notredame, C. Use of ChIP-Seq data for the design of a multiple promoter-alignment method. Nucleic Acids Res., 40(7):e52 (2012), PMID:22230796
Chang, J.-M., Di Tommaso, P., Taly, J.-F., Notredame, C. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinformatics, 13 Suppl 4:S1 (2012). PMID:22536955
Di Tommaso, P., Orobitg, M., Guirado, F., Cores, F., Espinosa, T., Notredame, C. Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics, 26(15):1903-1904 (2010). PMID:20605929
Wilm, A., Higgins, D.G., Notredame, C. R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36(9):e52 (2008), PMID:18420654
Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., Keduas, V., Notredame. C. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res., 34:W604-W608 (2006), PMID:16845081
Wallace, I.M., O’Sullivan, O., Higgins, D.G., Notredame, C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34(6):1692-1699 (2006), PMID:16556910
O’Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., Notredame, C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340(2):385-395 (2004). PMID: 15201059
O’Sullivan, O., Zehnder, M., Higgins, D.G., Bucher, P., Grosdidier, A., Notredame, C. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics, 19 Suppl 1:i215-i221 (2003). PMID:12855461
Notredame, C. Mocca: semi-automatic method for domain hunting. Bioinformatics, 17(4):373-374 (2001). PMID: 11301309
Notredame, C., Higgins, D.G., Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302(1):205-217 (2000). PMID: 10964570
Notredame, C., Holm, L., Higgins, D.G. COFFEE: an objective function for multiple sequence alignments. Bioinformatics, 14(5):407-422 (1998). PMID: 968205
T-Coffee Web Servers¶
Floden, E.W., Tommaso, P.D., Chatzou, M., Magis, C., Notredame, C., Chang, J.-M. PSI/TM-Coffee: a web server for fasta accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Res., 44(W1):W339-W343 (2016). PMID:27106060
Chang, J.-M.*, Tommaso P.*, Lefort, V., Gascuel, O., Notredame, C. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic Acids Research. 43(W1):W3-6 (2015). PMID: (*These two authors contribute equally)
Di Tommaso, P., Bussotti, G., Kemena, C., Capriotti, E., Chatzou, M., Prieto, P., Notredame, C. SARA-Coffee web server, a tool for computation of RNA sequence and structure multiple alignments. Nucleic Acids Res., 42(Web Server issue):W356-W360 (2014). PMID:24972831
Magis, C., Di Tommaso, P., Notredame, C. T-RMSD: a web server for automated fine-grained protein structural classifcation. Nucleic Acids Res., 41(Web Server issue):W358-W362 (2013). PMID:23716642
Rius, J., Cores, F., Solsona, F., van Hemert, J.I., Koetsier, J., Notredame, C. A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinformatics, 12:150 (2011). PMID:21569428
Di Tommaso, P., Moretti, S., Xenarios, I., Orobitg, M., Montanyola, A., Chang, J.-M., Taly, J.-F., Notredame, C. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res., 39(Web Server issue):W13-W17 (2011). PMID:21558174
Moretti, S., Wilm, A., Higgins, D.G., Xenarios, I., Notredame, C. R-Coffee: a web server for accurately aligning noncoding RNA sequences., Nucleic Acids Res., 36(Web Server issue):W10-W13 (2008). PMID:18483080
Moretti, S., Armougom, F., Wallace, I.M., Higgins, D.G., Jongeneel, C.V., Notredame, C. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res., 35(Web Server issue):W645-W648 (2007). PMID:17526519
Moretti, S., Reinier, F., Poirot, O., Armougom, F., Audic, S., Keduas, V., Notredame, C. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res., 34(Web server issue):W600-W603 (2006), PMID:16845080
Armougom, F., Moretti, S., Keduas, V., Notredame, C. The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics, 22(14):e35-e39 (2006). PMID:16873492
Armougom, F., Poirot, O., Moretti, S., Higgins, D.G., Bucher, P., Keduas, V., Notredame, C. APDB: a web server to evaluate the accuracy of the sequence alignments using structural information. Bioinformatics, 22(19):2439-2440 (2006). PMID:17032685
Claude, J.B., Suhre, K., Notredame, C., Claverie, J.M., Abergel C. CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res., 32(Web Server issue):W606-9 (2004). PMID:15215460
Poirot, O., Suhre, K., Abergel, C., O’Toole, E., Notredame, C. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res., 32(Web Server issue):W37-40 (2004). PMID: 15215345
Poirot, O., O’Toole, E., Notredame, C. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res., Jul 1;31(13):3503-6 (2003). PMID: 12824354
T-Coffee Tools For MSA Evaluation¶
Chang, J.-M., Tommaso, P., Notredame, C. TCS: a new Multiple Sequence Alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Molecular Biology and Evolution, 31(6):1625-37 (2014). PMID:24694831
Kemena, C., Taly, J.-F., Kleinjung, J., Notredame, C. STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinformatics, 27(24):3385-3391 (2011). PMID:220339207
Magis, C., Stricher, F., van der Sloot, A.M., Serrano, L., Notredame, C. T-RMSD: a fine-grained, structure based classification method and its application to the functional characterization of TNF receptors. J. Mol. Biol., 400(3):605-617 (2010), PMID:20471393
Armougom, F., Moretti, S., Keduas, V., Notredame, C. The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics, 22(14):e35-e39 (2006), PMID:16873492
Reviews, Briefings & Books¶
Chatzou, M., Magis, C., Chang, J.-M., Kemena, C., Bussotti, G., Erb, I., Notredame, C. Multiple sequence alignment modeling: methods and applications. Brief Bioinform., pii: bbv099 (2015). PMID:26615024
Magis, C., Taly, J.-F., Bussotti, G., Chang, J.M., Di Tommaso, P., Erb, I., Espinosa-Carrasco, J., Notredame, C. T-Coffee: tree-based consistency objective function for alignment evaluation. Methods Mol. Biol., 1079:117-129 (2014). PMID:24170398
Taly, J.-F.*, Magis, C.*, Bussotti, G., Chang, J.-M., Di Tommaso, P., Erb, I., Espinosa-Carrasco, J., Kemena, C., Notredame, C. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nature Protocols, 1669-1682 (2011), PMID:21979275 (*These two authors contribute equally)
Notredame, C. Computing multiple sequence/structure alignments with the T-Coffee package. Curr. Protoc. Bioinformatics, Chapter 3, Unit 3.8.1-25 (2010). PMID:20205190
Kemena, C., Notredame, C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25(19):2455-2465 (2009). PMID:19648142
Notredame, C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol., 3(8):e123 (2007). PMID:17784778
Notredame, C., Suhre, K. Computing multiple sequence/structure alignments with the T-Coffee package. Curr. Protoc. Bioinformatics, Chapter 3:Unit 3.8 (2004), PMID:18428722
Notredame, C., Abergel, C. Using multiple alignment methods to assess the quality of genomic data analysis. In: Andrade MA, editor. Bioinformatics and genomes: current perspectives. Wymondham (UK): Horizon Scientific Press,30–50 (2003).
Notredame, C. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics, 3(1):131-144 (2002). PMID:11966409