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Gibson TeamPublications

Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems.
Weatheritt, R.J., Gibson, T.J. & Babu, M.M.
Nat Struct Mol Biol. 2014 Aug 24. doi: 10.1038/nsmb.2876. Europe PMC

Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer?
Uyar, B., Weatheritt, R.J., Dinkel, H., Davey, N.E. & Gibson, T.J.
Mol Biosyst. 2014 Jul 24. Europe PMC

A Million Peptide Motifs for the Molecular Biologist.
Tompa, P., Davey, N.E., Gibson, T.J. & Babu, M.M.
This is a review article.
Mol Cell. 2014 Jul 17;55(2):161-169. doi: 10.1016/j.molcel.2014.05.032. Europe PMC

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation.
Van Roey, K., Uyar, B., Weatheritt, R.J., Dinkel, H., Seiler, M., Budd, A., Gibson, T.J. & Davey, N.E.
Chem Rev. 2014 Jun 13. Europe PMC

The eukaryotic linear motif resource ELM: 10 years and counting.
Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T., Kruger, D., Grebnev, G., Kuban, M., Strumillo, M., Uyar, B., Budd, A., Altenberg, B., Seiler, M., Chemes, L.B., Glavina, J., Sanchez, I.E., Diella, F. & Gibson, T.J.
Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: 10.1093/nar/gkt1047.Epub 2013 Nov 7. Europe PMC

Elution profile analysis of SDS-induced subcomplexes by quantitative mass spectrometry.
Texier, Y., Toedt, G., Gorza, M., Mans, D.A., van Reeuwijk, J., Horn, N., Willer, J., Katsanis, N., Roepman, R., Gibson, T.J., Ueffing, M. & Boldt, K.
Mol Cell Proteomics. 2014 May;13(5):1382-91. doi: 10.1074/mcp.O113.033233. Epub2014 Feb 21. Europe PMC

Drift and conservation of differential exon usage across tissues in primate species.
Reyes, A., Anders, S., Weatheritt, R.J., Gibson, T.J., Steinmetz, L.M. & Huber, W.
Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15377-82. doi:10.1073/pnas.1307202110. Epub 2013 Sep 3. Europe PMC

The transience of transient overexpression.
Gibson, T.J., Seiler, M. & Veitia, R.A.
Nat Methods. 2013 Aug;10(8):715-21. doi: 10.1038/nmeth.2534. Europe PMC

The switches.ELM resource: a compendium of conditional regulatory interaction interfaces.
Van Roey, K., Dinkel, H., Weatheritt, R.J., Gibson, T.J. & Davey, N.E.
Sci Signal. 2013 Apr 2;6(269):rs7. doi: 10.1126/scisignal.2003345. Europe PMC

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions.
Davey, N.E., Cowan, J.L., Shields, D.C., Gibson, T.J., Coldwell, M.J. & Edwards, R.J.
Nucleic Acids Res. 2012 Nov 1;40(21):10628-41. doi: 10.1093/nar/gks854. Epub 2012Sep 12. Europe PMC

A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins.
Jiang, K., Toedt, G., Montenegro Gouveia, S., Davey, N.E., Hua, S., van der Vaart, B., Grigoriev, I., Larsen, J., Pedersen, L.B., Bezstarosti, K., Lince-Faria, M., Demmers, J., Steinmetz, M.O., Gibson, T.J. & Akhmanova, A.
Curr Biol. 2012 Oct 9;22(19):1800-7. doi: 10.1016/j.cub.2012.07.047. Epub 2012Aug 9. Europe PMC

RACK1 research - ships passing in the night?
Gibson, T.J.
FEBS Lett. 2012 Aug 14;586(17):2787-9. doi: 10.1016/j.febslet.2012.04.048. Epub2012 May 8. Europe PMC

Linear motifs: lost in (pre)translation.
Weatheritt, R.J. & Gibson, T.J.
Trends Biochem Sci. 2012 Aug;37(8):333-41. doi: 10.1016/j.tibs.2012.05.001. Epub2012 Jun 15. Europe PMC

Prion infected rhesus monkeys to study differential transcription of Alu DNA elements and editing of Alu transcripts in neuronal cells and blood cells.
Kiesel, P., Bodemer, W., Gibson, T.J., Zischler, H. & Kaup, F.J.
J Med Primatol. 2012 Jun;41(3):176-82. doi: 10.1111/j.1600-0684.2012.00535.x.Epub 2012 Mar 2. Europe PMC

iELM--a web server to explore short linear motif-mediated interactions.
Weatheritt, R.J., Jehl, P., Dinkel, H. & Gibson, T.J.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W364-9. doi: 10.1093/nar/gks444.Epub 2012 May 25. Europe PMC

Linear motifs confer functional diversity onto splice variants.
Weatheritt, R.J., Davey, N.E. & Gibson, T.J.
Nucleic Acids Res. 2012 Aug;40(15):7123-31. doi: 10.1093/nar/gks442. Epub 2012May 25. Europe PMC

Motif switches: decision-making in cell regulation.
Van Roey, K., Gibson, T.J. & Davey, N.E.
Curr Opin Struct Biol. 2012 Jun;22(3):378-85. doi: 10.1016/ 2012 Apr 3. Europe PMC

The identification of short linear motif-mediated interfaces within the human interactome.
Weatheritt, R.J., Luck, K., Petsalaki, E., Davey, N.E. & Gibson, T.J.
Bioinformatics. 2012 Apr 1;28(7):976-82. doi: 10.1093/bioinformatics/bts072. Epub2012 Feb 10. Europe PMC

Attributes of short linear motifs.
Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H. & Gibson, T.J.
Mol Biosyst. 2012 Jan;8(1):268-81. doi: 10.1039/c1mb05231d. Epub 2011 Sep 12. Europe PMC

ELM--the database of eukaryotic linear motifs.
Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., Jodicke, L., Dammert, M.A., Schroeter, C., Hammer, M., Schmidt, T., Jehl, P., McGuigan, C., Dymecka, M., Chica, C., Luck, K., Via, A., Chatr-Aryamontri, A., Haslam, N., Grebnev, G., Edwards, R.J., Steinmetz, M.O., Meiselbach, H., Diella, F. & Gibson, T.J.
Nucleic Acids Res. 2012 Jan 1;40(D1):D242-D251. Epub 2011 Nov 21. Europe PMC

A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta).
Kiesel, P., Kues, A., Kaup, F.J., Bodemer, W., Gibson, T.J. & Zischler, H.
J Toxicol Environ Health A. 2012;75(7):391-401. doi:10.1080/15287394.2012.670896. Europe PMC

Possible editing of Alu transcripts in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).
Kiesel, P., Gibson, T.J., Ciesielczyk, B., Bodemer, M., Kaup, F.J., Bodemer, W., Zischler, H. & Zerr, I.
J Toxicol Environ Health A. 2011 Jan;74(2-4):88-95. Europe PMC

Phospho.ELM: a database of phosphorylation sites--update 2011.
Dinkel, H., Chica, C., Via, A., Gould, C.M., Jensen, L.J., Gibson, T.J. & Diella, F.
Nucleic Acids Res. 2011 Jan;39(Database issue):D261-7. Epub 2010 Nov 9. Europe PMC

From sequence to structural analysis in protein phosphorylation motifs.
Via, A., Diella, F., Gibson, T.J. & Helmer-Citterich, M.
Front Biosci. 2011 Jan 1;16:1261-75. Europe PMC

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. & Higgins, D.G.
Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. Europe PMC

How viruses hijack cell regulation.
Davey, N.E., Trave, G. & Gibson, T.J.
Trends Biochem Sci. 2011 Mar;36(3):159-69. Epub 2010 Dec 9 Europe PMC

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.
Croset, V., Rytz, R., Cummins, S.F., Budd, A., Brawand, D., Kaessmann, H., Gibson, T.J. & Benton, R.
PLoS Genet. 2010 Aug 19;6(8). pii: e1001064. Europe PMC

EpiC: an open resource for exploring epitopes to aid antibody-based experiments.
Haslam, N.J. & Gibson, T.J.
J Proteome Res. 2010 Jul 2;9(7):3759-63. Europe PMC

Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD).
Kiesel, P., Gibson, T.J., Ciesielczyk, B., Bodemer, M., Kaup, F.J., Bodemer, W., Zischler, H. & Zerr, I.
Prion. 2010 Apr-Jun;4(2):87-93. Epub 2010 Apr 5. Europe PMC

ELM: the status of the 2010 eukaryotic linear motif resource.
Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Sayadi, A., Bryne, J.C., Chica, C., Seiler, M., Davey, N.E., Haslam, N., Weatheritt, R.J., Budd, A., Hughes, T., Pas, J., Rychlewski, L., Trave, G., Aasland, R., Helmer-Citterich, M., Linding, R. & Gibson, T.J.
Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016.Epub 2009 Nov 17. Europe PMC

A community standard format for the representation of protein affinity reagents.
Gloriam, D.E., Orchard, S., Bertinetti, D., Bjorling, E., Bongcam-Rudloff, E., Borrebaeck, C.A., Bourbeillon, J., Bradbury, A.R., de Daruvar, A., Dubel, S., Frank, R., Gibson, T.J., Gold, L., Haslam, N., Herberg, F.W., Hiltke, T., Hoheisel, J.D., Kerrien, S., Koegl, M., Konthur, Z., Korn, B., Landegren, U., Montecchi-Palazzi, L., Palcy, S., Rodriguez, H., Schweinsberg, S., Sievert, V., Stoevesandt, O., Taussig, M.J., Ueffing, M., Uhlen, M., van der Maarel, S., Wingren, C., Woollard, P., Sherman, D.J. & Hermjakob, H.
Mol Cell Proteomics. 2010 Jan;9(1):1-10. doi: 10.1074/mcp.M900185-MCP200. Epub2009 Aug 11. Europe PMC

Cell regulation: determined to signal discrete cooperation.
Gibson, T.J.
Trends Biochem Sci. 2009 Oct;34(10):471-82. Epub 2009 Sep 8. Europe PMC

Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60.
Corsini, L., Hothorn, M., Stier, G., Rybin, V., Scheffzek, K., Gibson, T.J. & Sattler, M.
J Biol Chem. 2009 Jan 2;284(1):630-9. doi: 10.1074/jbc.M805395200. Epub 2008 Oct29. Europe PMC

KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors.
Diella, F., Chabanis, S., Luck, K., Chica, C., Ramu, C., Nerlov, C. & Gibson, T.J.
Bioinformatics. 2009 Jan 1;25(1):1-5. Epub 2008 Nov 24. Europe PMC

A structure filter for the Eukaryotic Linear Motif Resource.
Via, A., Gould, C.M., Gemund, C., Gibson, T.J. & Helmer-Citterich, M.
BMC Bioinformatics. 2009 Oct 24;10:351. Europe PMC

Phosphorylation of s776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors.
de Chiara, C., Menon, R.P., Strom, M., Gibson, T.J. & Pastore, A.
PLoS One. 2009 Dec 23;4(12):e8372. Europe PMC

Evidence for the concerted evolution between short linear protein motifs and their flanking regions.
Chica, C., Diella, F. & Gibson, T.J.
PLoS One. 2009 Jul 8;4(7):e6052. Europe PMC

Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation.
Schallus, T., Jaeckh, C., Feher, K., Palma, A.S., Liu, Y., Simpson, J.C., Mackeen, M., Stier, G., Gibson, T.J., Feizi, T., Pieler, T. & Muhle-Goll, C.
Mol Biol Cell. 2008 Aug;19(8):3404-14. Epub 2008 Jun 4. Europe PMC

A careful disorderliness in the proteome: sites for interaction and targets for future therapies.
Russell, R.B. & Gibson, T.J.
FEBS Lett. 2008 Apr 9;582(8):1271-5. doi: 10.1016/j.febslet.2008.02.027. Epub2008 Feb 20. Europe PMC

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.
Michael, S., Trave, G., Ramu, C., Chica, C. & Gibson, T.J.
Bioinformatics. 2008 Feb 15;24(4):453-7. Epub 2008 Jan 9. Europe PMC

Phospho.ELM: a database of phosphorylation sites--update 2008.
Diella, F., Gould, C.M., Chica, C., Via, A. & Gibson, T.J.
Nucleic Acids Res. 2008 Jan;36(Database issue):D240-4. Epub 2007 Oct 25. Europe PMC

A new protein linear motif benchmark for multiple sequence alignment software.
Perrodou, E., Chica, C., Poch, O., Gibson, T.J. & Thompson, J.D.
BMC Bioinformatics. 2008 Apr 25;9:213. Europe PMC

Understanding eukaryotic linear motifs and their role in cell signaling and regulation.
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G. & Gibson, T.J.
Front Biosci. 2008 May 1;13:6580-603. Europe PMC

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica, C., Labarga, A., Gould, C.M., Lopez, R. & Gibson, T.J.
BMC Bioinformatics. 2008 May 6;9:229. Europe PMC

Clustal W and Clustal X version 2.0.
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. & Higgins, D.G.
Bioinformatics. 2007 Nov 1;23(21):2947-8. Epub 2007 Sep 10. Europe PMC

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig, M.J., Stoevesandt, O., Borrebaeck, C.A., Bradbury, A.R., Cahill, D., Cambillau, C., de Daruvar, A., Dubel, S., Eichler, J., Frank, R., Gibson, T.J., Gloriam, D., Gold, L., Herberg, F.W., Hermjakob, H., Hoheisel, J.D., Joos, T.O., Kallioniemi, O., Koegll, M., Konthur, Z., Korn, B., Kremmer, E., Krobitsch, S., Landegren, U., van der Maarel, S., McCafferty, J., Muyldermans, S., Nygren, P.A., Palcy, S., Pluckthun, A., Polic, B., Przybylski, M., Saviranta, P., Sawyer, A., Sherman, D.J., Skerra, A., Templin, M., Ueffing, M. & Uhlen, M.
Nat Methods. 2007 Jan;4(1):13-7. Europe PMC

Systematic discovery of new recognition peptides mediating protein interaction networks.
Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, T.J., Lewis, J.D., Serrano, L. & Russell, R.B.
PLoS Biol. 2005 Dec;3(12):e405. Epub 2005 Nov 15. Europe PMC

Anopheles gambiae SRPN2 facilitates midgut invasion by the malaria parasite Plasmodium berghei.
Michel, K., Budd, A., Pinto, S., Gibson, T.J. & Kafatos, F.C.
EMBO Rep 2005 Sep;6(9):891-7. Europe PMC

Patterns and clusters within the PSM column in TiBS, 1992-2004.
McEntyre, J.R. & Gibson, T.J.
Trends Biochem Sci 2004 Dec;29(12):627-33. Europe PMC

The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre.
Menon, R.P., Gibson, T.J. & Pastore, A.
J Mol Biol 2004 Oct 8;343(1):43-53. Europe PMC

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.
Diella, F., Cameron, S., Gemund, C., Linding, R., Via, A., Kuster, B., Sicheritz-Ponten, T., Blom, N. & Gibson, T.J.
BMC Bioinformatics 2004 Jun 22;5(1):79. Europe PMC

Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.
Ragvin, A., Valvatne, H., Erdal, S., Arskog, V., Tufteland, K.R., Breen, K., OYan, A.M., Eberharter, A., Gibson, T.J., Becker, P.B. & Aasland, R.
J Mol Biol 2004 Apr 2;337(4):773-88. Europe PMC

Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?
Budd, A., Blandin, S., Levashina, E.A. & Gibson, T.J.
Genome Biol 2004;5(6):R38. Epub 2004 May 26. Europe PMC

Protein disorder prediction. Implications for structural proteomics.
Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J. & Russell, R.B.
Structure (Camb) 2003 Nov;11(11):1453-9. Europe PMC

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuster, B., Helmer-Citterich, M., Hunter, W.N., Aasland, R. & Gibson, T.J.
Nucleic Acids Res 2003 Jul 1;31(13):3625-30. Europe PMC

Multiple sequence alignment with the Clustal series of programs.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. & Thompson, J.D.
Nucleic Acids Res 2003 Jul 1;31(13):3497-500. Europe PMC

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.
Bimpikis, K., Budd, A., Linding, R. & Gibson, T.J.
Nucleic Acids Res 2003 Jul 1;31(13):3792-4. Europe PMC

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A., Snel, B., Bork, P. & Gibson, T.J.
Hum Mol Genet 2001 Oct 1;10(21):2463-8. Europe PMC

The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin.
Moreira, M.C., Barbot, C., Tachi, N., Kozuka, N., Uchida, E., Gibson, T., Mendonca, P., Costa, M., Barros, J., Yanagisawa, T., Watanabe, M., Ikeda, Y., Aoki, M., Nagata, T., Coutinho, P., Sequeiros, J. & Koenig, M.
Nat Genet 2001 Oct;29(2):189-93. Europe PMC

The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.
Bottomley, M.J., Collard, M.W., Huggenvik, J.I., Liu, Z., Gibson, T.J. & Sattler, M.
Nat Struct Biol 2001 Jul;8(7):626-33. Europe PMC

Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries.
Gemund, C., Ramu, C., Altenberg-Greulich, B. & Gibson, T.J.
Nucleic Acids Res 2001 Mar 15;29(6):1272-7. Europe PMC

RuNAway Disease: A two cycle model for transmissible spongiform encephalopathies (TSEs) wherein SINE proliferation drives PrP overproduction.
Gibson, T.J.
Genome Biol 2001;2(7):Preprint 0006. Europe PMC

Object-oriented parsing of biological databases with python.
Ramu, C., Gemund, C. & Gibson, T.J.
Bioinformatics 2000 Jul;16(7):628-38 Europe PMC

An estimate of large-scale sequencing accuracy.
Hill, F., Gemund, C., Benes, V., Ansorge, W. & Gibson, T.J.
EMBO Rep. 2000 Jul;1(1):29-31. Europe PMC

Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A., Ponting, C.P., Gibson, T.J. & Bork, P.
J Mol Biol 2000 May 5;298(3):521-37 Europe PMC

Evidence in favour of ancient octaploidy in the vertebrate genome.
Gibson, T.J. & Spring, J.
Biochem Soc Trans 2000 Feb;28(2):259-64. Europe PMC

Assignment of the 1H, 15N, and 13C resonances of the C-terminal domain of frataxin, the protein responsible for Friedreich ataxia
Musco, G., de Tommasi, T., Stier, G., Kolmerer, B., Bottomley, M., Adinolfi, S., Muskett, F.W., Gibson, T.J., Frenkiel, T.A. & Pastore, A.
J Biomol NMR 1999 Sep;15(1):87-8 Europe PMC

Formin defines a large family of morphoregulatory genes and functions in establishment of the polarising region.
Zeller, R., Haramis, A.G., Zuniga, A., McGuigan, C., Dono, R., Davidson, G., Chabanis, S. & Gibson, T.
Cell Tissue Res 1999 Mar 29 296(1) 85-93 Europe PMC

Multiple sequence alignment with Clustal X.
Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G. & Gibson, T.J.
Trends Biochem Sci 1998 Oct 23(10) 403-405 Europe PMC

A new method for isolating tyrosine kinase substrates used to identify fish, an SH3 and PX domain-containing protein, and Src substrate.
Lock, P., Abram, C.L., Gibson, T. & Courtneidge, S.A.
EMBO J 1998 Aug 3 17(15) 4346-4357 Europe PMC

The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor
Gibson, T.J., Ramu, C., Gemund, C. & Aasland, R.
Trends Biochem Sci 1998 Jul 23(7) 242-244 Europe PMC

Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins.
Gibson, T.J. & Spring, J.
This is a review article.
Trends Genet 1998 Feb 14(2) 46-49 Europe PMC

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G.
Nucleic Acids Res. 1997 Dec 15;25(24):4876-82. Europe PMC

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.
Birney, E., Thompson, J.D. & Gibson, T.J.
Nucleic Acids Res 1996 Jul 15;24(14):2730-9 Europe PMC

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson, J.D., Higgins, D.G. & Gibson, T.J.
Nucleic Acids Res 1994 Nov 11;22(22):4673-80 Europe PMC