Bioinformatics Advance Access originally published online on September 10, 2007
Bioinformatics 2007 23(21):2947-2948; doi:10.1093/bioinformatics/btm404
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Clustal W and Clustal X version 2.0
1The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland, 2Laboratoire de Biologie et Genomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France, 3European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and 4EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK
*To whom correspondence should be addressed.
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ABSTRACT |
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 TOP ABSTRACT 1 INTRODUCTION2 NEW FEATURESACKNOWLEDGEMENTREFERENCES |
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Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: clustalw{at}ucd.ie
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1 INTRODUCTION |
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TOPABSTRACT1 INTRODUCTION2 NEW FEATURESACKNOWLEDGEMENTREFERENCES |
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Multiple sequence alignments are now one of the most widely used bioinformatics analyses. They are needed routinely as parts of more complicated analyses or analysis pipelines and there are several very widely used packages, e.g. Clustal W (Thompson et al., 1994), Clustal X (Thompson et al., 1997), T-Coffee (Notredame et al., 2000), MAFFT (Katoh et al., 2002) and MUSCLE (Edgar, 2004). Clustal is also the oldest of the currently most widely used programs having been first distributed by post on floppy disks in the late 1980s. It was initially written in Microsoft Fortran for MS-DOS and originally ran on IBM compatible personal computers as four separate executable programs, Clustal1–Clustal4 (Higgins and Sharp, 1988, 1989). These were later rewritten in C and merged into a single program, Clustal V (Higgins et al., 1992), that was distributed for VAX/VMS, Unix, Apple Macintosh and IBM compatible PCs. These programs were distributed from the EMBL File server (Stoehr and Omond, 1989), an e-mail and FTP server, based at the EMBL in Heidelberg, Germany.
The current Clustal programs all derive from Clustal W (Thompson et al., 1994), which incorporated a novel position-specific scoring scheme and a weighting scheme for down weighting over-represented sequence groups. The ‘W’ stands for ‘weights’. These programs have been amended and added to many times since 1994 in order to increase functionality and to increase sensitivity. The user-friendliness has also been greatly enhanced by the addition, in 1997, of a full graphical user interface (Thompson et al., 1997). This has made the code complicated to maintain and develop, as the graphical interface must be constantly modified and recompiled for new operating systems and desktop environments (Windows, Macintosh, VMS, Unix and Linux).
By the late 1990s, Clustal W and Clustal X were the most widely used multiple alignment programs. They were able to align medium-sized data sets very quickly and were easy to use. The alignments were of sufficient quality not to require manual editing or adjustment very often. This situation changed greatly with the appearance of the first custom made benchmark test set for multiple alignment programs, BAliBASE (Thompson et al., 1999). This was followed by the appearance of T-Coffee which was able to make very accurate alignments of very divergent proteins but only for small sets of sequences, given its high computational cost. With the increase in processing speed of desktop computers, and subsequent optimisation of the T-Coffee code, the latter is now practical for routine use on moderately sized alignment problems. More recently, MAFFT and MUSCLE appeared; which were, initially, at least as accurate as Clustal, in terms of alignment accuracy, but which were also extremely fast; and able to align many thousands of sequences. Over the past 4 or 5 years, these programs have also gradually become more and more accurate with difficult alignments. Nonetheless, Clustal W and Clustal X continue to be very widely used, increasingly on websites. The EBI Clustal site, gets literally millions of multiple alignment jobs per year.
It is in this context that we developed Clustal W 2.0 and Clustal X 2.0. These programs were rewritten in C++ with a simple object model in order to make it easier to maintain the code and more importantly, to make it easier to modify or even replace some of the alignment algorithms. We have produced two new programs which are very similar in look and feel to the older version 1.83 programs but which can now be managed more easily. We have also made some minor adjustments to the alignment algorithms. We have included new code for UPGMA guide trees as an alternative to the usual Neighbor-Joining guide trees. This helps speed up the alignment of extremely large data sets of tens of thousands of sequences. We have also included an iterative alignment facility to increase alignment accuracy.
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Clustal X 2.0 is the new version of the Clustal X graphical alignment tool. The original Clustal X was developed using NCBI's vibrant toolbox. The vibrant toolbox is no longer supported which led to problems compiling Clustal X on newer versions of operating systems. The graphical interface sections of Clustal X 2.0 have been completely rewritten using the Qt GUI toolbox. Qt is an easy-to-use, multi-platform C++ GUI toolkit. The code need only be compiled once on each of the platforms. The Qt toolbox provides a native look and feel on Windows, Linux and Mac platforms. Clustal X 2.0 has the same functionality as Clustal X.
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2 NEW FEATURES |
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TOPABSTRACT1 INTRODUCTION2 NEW FEATURESACKNOWLEDGEMENTREFERENCES |
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Two new options have been included in Clustal W 2.0, to allow faster alignment of very large data sets and to increase alignment accuracy. The default options of Clustal W And Clustal X 2.0 are the same as Clustal W 1.83, and will give the same alignment results.
The guide trees in Clustal have been calculated using the Neighbor-Joining (NJ) method, for the past 10 years or so. In the earliest versions of the program UPGMA was used. UPGMA is faster than NJ but prone to cluster long branches together when evolutionary rates are very unequal in different lineages. Both algorithms have complexity of O(N2) but UPGMA is faster for a given data set and the difference becomes pronounced with very large N. On a standard desktop PC, it is possible to cluster 10 000 sequences in less than a minute using UPGMA, while NJ would take over an hour. We have reimplemented a very efficient algorithm for UPGMA which can be called by using the command line option ‘-clustering=UPGMA’. It is marginally less accurate on the Balibase benchmark, but on large alignments (e.g. 10 000 globin sequences) this is offset by the savings in processing time (2 h versus 12 h).
Iteration is a quick and effective method of refining alignments. A ‘remove first’ iteration scheme, which optimizes the Weighted Sum of Pairs (WSP) score, has been included in this version of Clustal. During each iteration step, each sequence is removed from the alignment in turn and realigned. If the WSP score is reduced then the resulting alignment is retained. The iteration scheme can be used to either refine the final alignment or at each step in the progressive alignment. Iterating during the progressive alignment tends to be more accurate but also much more time consuming as there are 2N-3 nodes in the guide tree. The command line option ‘-Iteration=Alignment’ refines the final alignment, while the option ‘-Iteration=Tree’ incorporates the scheme into the progressive alignment. The number of iteration cycles is set via the command line option ‘-numiters’ (default is 3).
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ACKNOWLEDGEMENT |
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TOPABSTRACT1 INTRODUCTION2 NEW FEATURESACKNOWLEDGEMENTREFERENCES |
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This work was mainly funded by Science Foundation Ireland.
Conflict of Interest: none declared.
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FOOTNOTES |
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Associate Editor: Alex Bateman
Received on June 27, 2007; revised on August 3, 2007; accepted on August 3, 2007
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REFERENCES |
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TOPABSTRACT1 INTRODUCTION2 NEW FEATURESACKNOWLEDGEMENTREFERENCES |
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Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. (2004) 32:1792–1797.
Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene (1988) 73:237–244.[CrossRef][Web of Science][Medline]
Higgins DG, Sharp PM. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. (1989) 5:151–153.
Higgins DG, et al. CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. (1992) 8:189–191.
Katoh K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. (2002) 30:3059–3066.
Notredame C, et al. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. (2000) 302:205–217.[CrossRef][Web of Science][Medline]
Stoehr PJ, Omond RA. The EMBL Network File Server. Nucleic Acids Res. (1989) 17:6763–6764.
Thompson JD, et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. (1994) 22:4673–4680.
Thompson JD, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. (1997) 25:4876–4882.
Thompson JD, et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics (1999) 15:87–88.
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M. Novo, F. Bigey, E. Beyne, V. Galeote, F. Gavory, S. Mallet, B. Cambon, J.-L. Legras, P. Wincker, S. Casaregola, et al. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 PNAS, September 22, 2009; 106(38): 16333 - 16338. [Abstract] [Full Text] [PDF]
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K. L. Hailey, S. Li, M. D. Andersen, M. Roy, V. L. Woods Jr, and P. A. Jennings Pro-interleukin (IL)-1{beta} Shares a Core Region of Stability as Compared with Mature IL-1{beta} While Maintaining a Distinctly Different Configurational Landscape: A COMPARATIVE HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY STUDY J. Biol. Chem., September 18, 2009; 284(38): 26137 - 26148. [Abstract] [Full Text] [PDF]
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M. Rho and H. Tang MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes Nucleic Acids Res., September 17, 2009; (2009) gkp752v1. [Abstract] [Full Text] [PDF]
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C. Linke, T. T. Caradoc-Davies, P. G. Young, T. Proft, and E. N. Baker The Laminin-Binding Protein Lbp from Streptococcus pyogenes Is a Zinc Receptor J. Bacteriol., September 15, 2009; 191(18): 5814 - 5823. [Abstract] [Full Text] [PDF]
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M. Avila-Perez, J. Vreede, Y. Tang, O. Bende, A. Losi, W. Gartner, and K. Hellingwerf In Vivo Mutational Analysis of YtvA from Bacillus subtilis: MECHANISM OF LIGHT ACTIVATION OF THE GENERAL STRESS RESPONSE J. Biol. Chem., September 11, 2009; 284(37): 24958 - 24964. [Abstract] [Full Text] [PDF]
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J. Chun, C. J. Grim, N. A. Hasan, J. H. Lee, S. Y. Choi, B. J. Haley, E. Taviani, Y.-S. Jeon, D. W. Kim, J.-H. Lee, et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae PNAS, September 8, 2009; 106(36): 15442 - 15447. [Abstract] [Full Text] [PDF]
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S. A. Headley, A. M. Amude, A. F. Alfieri, A. P. F.R.L. Bracarense, A. A. Alfieri, and B. A. Summers Molecular detection of Canine distemper virus and the immunohistochemical characterization of the neurologic lesions in naturally occurring old dog encephalitis J Vet Diagn Invest, September 1, 2009; 21(5): 588 - 597. [Abstract] [Full Text] [PDF]
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S. C. Leao, E. Tortoli, C. Viana-Niero, S. Y. M. Ueki, K. V. B. Lima, M. L. Lopes, J. Yubero, M. C. Menendez, and M. J. Garcia Characterization of Mycobacteria from a Major Brazilian Outbreak Suggests that Revision of the Taxonomic Status of Members of the Mycobacterium chelonae-M. abscessus Group Is Needed J. Clin. Microbiol., September 1, 2009; 47(9): 2691 - 2698. [Abstract] [Full Text] [PDF]
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N. O. G. Jorgensen, K. K. Brandt, O. Nybroe, and M. Hansen Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2195 - 2199. [Abstract] [Full Text] [PDF]
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 S. T. Gregory, H. Demirci, R. Belardinelli, T. Monshupanee, C. Gualerzi, A. E. Dahlberg, and G. Jogl Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG RNA, September 1, 2009; 15(9): 1693 - 1704. [Abstract] [Full Text] [PDF]
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T. Phan, R. K. F. Beran, C. Peters, I. C. Lorenz, and B. D. Lindenbach Hepatitis C Virus NS2 Protein Contributes to Virus Particle Assembly via Opposing Epistatic Interactions with the E1-E2 Glycoprotein and NS3-NS4A Enzyme Complexes J. Virol., September 1, 2009; 83(17): 8379 - 8395. [Abstract] [Full Text] [PDF]
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P. T. Beernink and D. M. Granoff The modular architecture of meningococcal factor H-binding protein Microbiology, September 1, 2009; 155(9): 2873 - 2883. [Abstract] [Full Text] [PDF]
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P. Salah, M. Bisaglia, P. Aliprandi, M. Uzan, C. Sizun, and F. Bontems Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis Nucleic Acids Res., September 1, 2009; 37(16): 5578 - 5588. [Abstract] [Full Text] [PDF]
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F. M. Dwivany, D. Yulia, R. A. Burton, N. J. Shirley, S. M. Wilson, G. B. Fincher, A. Bacic, E. Newbigin, and M. S. Doblin The CELLULOSE-SYNTHASE LIKE C (CSLC) Family of Barley Includes Members that Are Integral Membrane Proteins Targeted to the Plasma Membrane Mol Plant, September 1, 2009; 2(5): 1025 - 1039. [Abstract] [Full Text] [PDF]
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F. Bollig, B. Perner, B. Besenbeck, S. Kothe, C. Ebert, S. Taudien, and C. Englert A highly conserved retinoic acid responsive element controls wt1a expression in the zebrafish pronephros Development, September 1, 2009; 136(17): 2883 - 2892. [Abstract] [Full Text] [PDF]
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N. Conde e Silva, I. R. Goncalves, M. Lemaire, E. Lesuisse, J. M. Camadro, and P. L. Blaiseau KlAft, the Kluyveromyces lactis Ortholog of Aft1 and Aft2, Mediates Activation of Iron-Responsive Transcription Through the PuCACCC Aft-Type Sequence Genetics, September 1, 2009; 183(1): 93 - 106. [Abstract] [Full Text] [PDF]
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S. Teotia and R. S. Lamb The Paralogous Genes RADICAL-INDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 Have Partially Redundant Functions during Arabidopsis Development Plant Physiology, September 1, 2009; 151(1): 180 - 198. [Abstract] [Full Text] [PDF]
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T. J. Moriarty and G. Chaconas Identification of the Determinant Conferring Permissive Substrate Usage in the Telomere Resolvase, ResT J. Biol. Chem., August 28, 2009; 284(35): 23293 - 23301. [Abstract] [Full Text] [PDF]
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M. S. Schonauer, A. J. Kastaniotis, V. A. S. Kursu, J. K. Hiltunen, and C. L. Dieckmann Lipoic Acid Synthesis and Attachment in Yeast Mitochondria J. Biol. Chem., August 28, 2009; 284(35): 23234 - 23242. [Abstract] [Full Text] [PDF]
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D. Albinsky, M. Kusano, M. Higuchi, N. Hayashi, M. Kobayashi, A. Fukushima, M. Mori, T. Ichikawa, K. Matsui, H. Kuroda, et al. Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism Mol Plant, August 26, 2009; (2009) ssp069v1. [Abstract] [Full Text] [PDF]
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L. Malki, M. Yanku, I. Borovok, G. Cohen, M. Mevarech, and Y. Aharonowitz Identification and Characterization of gshA, a Gene Encoding the Glutamate-Cysteine Ligase in the Halophilic Archaeon Haloferax volcanii J. Bacteriol., August 15, 2009; 191(16): 5196 - 5204. [Abstract] [Full Text] [PDF]
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J. Gury, H. Seraut, N. P. Tran, L. Barthelmebs, S. Weidmann, P. Gervais, and J.-F. Cavin Inactivation of PadR, the Repressor of the Phenolic Acid Stress Response, by Molecular Interaction with Usp1, a Universal Stress Protein from Lactobacillus plantarum, in Escherichia coli Appl. Envir. Microbiol., August 15, 2009; 75(16): 5273 - 5283. [Abstract] [Full Text] [PDF]
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J. L. Burns and T. J. DiChristina Anaerobic Respiration of Elemental Sulfur and Thiosulfate by Shewanella oneidensis MR-1 Requires psrA, a Homolog of the phsA Gene of Salmonella enterica Serovar Typhimurium LT2 Appl. Envir. Microbiol., August 15, 2009; 75(16): 5209 - 5217. [Abstract] [Full Text] [PDF]
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Z. Zhang, X. Zhu, L. M. Stevens, and D. Stein Distinct functional specificities are associated with protein isoforms encoded by the Drosophila dorsal-ventral patterning gene pipe Development, August 15, 2009; 136(16): 2779 - 2789. [Abstract] [Full Text] [PDF]
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C. P. Walsh, A. Davies, A. J. Butcher, A. C. Dolphin, and A. Kitmitto Three-dimensional Structure of CaV3.1: COMPARISON WITH THE CARDIAC L-TYPE VOLTAGE-GATED CALCIUM CHANNEL MONOMER ARCHITECTURE J. Biol. Chem., August 14, 2009; 284(33): 22310 - 22321. [Abstract] [Full Text] [PDF]
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A. Reymer, K. Frykholm, K. Morimatsu, M. Takahashi, and B. Norden From the Cover: Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy PNAS, August 11, 2009; 106(32): 13248 - 13253. [Abstract] [Full Text] [PDF]
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Q. H. Christensen and J. E. Cronan The Thermoplasma acidophilum LplA-LplB Complex Defines a New Class of Bipartite Lipoate-protein Ligases J. Biol. Chem., August 7, 2009; 284(32): 21317 - 21326. [Abstract] [Full Text] [PDF]
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 S. K. Krueger, M. C. Henderson, L. K. Siddens, J. E. VanDyke, A. D. Benninghoff, P. A. Karplus, B. Furnes, D. Schlenk, and D. E. Williams Characterization of Sulfoxygenation and Structural Implications of Human Flavin-Containing Monooxygenase Isoform 2 (FMO2.1) Variants S195L and N413K Drug Metab. Dispos., August 1, 2009; 37(8): 1785 - 1791. [Abstract] [Full Text] [PDF]
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M. J. Lace, C. Isacson, J. R. Anson, A. T. Lorincz, S. P. Wilczynski, T. H. Haugen, and L. P. Turek Upstream Regulatory Region Alterations Found in Human Papillomavirus Type 16 (HPV-16) Isolates from Cervical Carcinomas Increase Transcription, ori Function, and HPV Immortalization Capacity in Culture J. Virol., August 1, 2009; 83(15): 7457 - 7466. [Abstract] [Full Text] [PDF]
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K. E. Varley, D. G. Mutch, T. B. Edmonston, P. J. Goodfellow, and R. D. Mitra Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing Nucleic Acids Res., August 1, 2009; 37(14): 4603 - 4612. [Abstract] [Full Text] [PDF]
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S. Spork, J. A. Hiss, K. Mandel, M. Sommer, T. W. A. Kooij, T. Chu, G. Schneider, U. G. Maier, and J. M. Przyborski An Unusual ERAD-Like Complex Is Targeted to the Apicoplast of Plasmodium falciparum Eukaryot. Cell, August 1, 2009; 8(8): 1134 - 1145. [Abstract] [Full Text] [PDF]
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 R. Lucking, J. D. Lawrey, M. Sikaroodi, P. M. Gillevet, J. L. Chaves, H. J. M. Sipman, and F. Bungartz Do lichens domesticate photobionts like farmers domesticate crops? Evidence from a previously unrecognized lineage of filamentous cyanobacteria Am. J. Botany, August 1, 2009; 96(8): 1409 - 1418. [Abstract] [Full Text] [PDF]
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