Appendix: Software 25 [ ] A l t e r t h e f i l e m o d u l e . p m a n d p o s s i b l y w r a p p e r . pl , l o c a t e d i n / u s r / o p t / w w w / cgi−b i n / s o a p / w s / q u a s i / [ S E R V I C E ] / [ W S ] / 26 [ ] A l t e r t h e e x a m p l e s o t h a t i t c o n t a i n s a r e l e v a n t e x a m p l e f o r y o u r s e r v i c e . 27 [ ] A l t e r t h e i n c l u d e . h t m l s o t h a t i t d e s c r i b e s t h e u s a g e o f t h e e x a m p l e s c r i p t 28 [ ] O n c e y o u a r e h a p p y w i t h t h e i m p l e m e n t a t i o n , r e m o v e t h e f l a g ” i n t e r n a l _ o n l y ” f r o m m y s q l . W e b S e r v i c e s . s e r v i c e s 29 a n d c h a n g e t h e d e s i r e d d e s c r i p t i o n f o r y o u r s e r v i c e ( i n f i e l d ’ d e s c r i p t i o n ’ ) 30 31 O P T I O N S 32 −n S E R V I C E N A M E 33 C a s e −s e n s i t i v e s e r v i c e n a m e , e . g . S i g n a l P 34 35 −v V E R S I O N 36 T h e v e r s i o n o f t h e s e r v i c e i n t h e f o r m X . Y , e . g . 1 . 2 37 38 −w W S N U M B E R 39 T h i s i s t h e i m p l e m e n t a t i o n n u m b e r f o r t h i s s e r v i c e a n d v e r s i o n . T h e n u m b e r 40 s t a r t s a t z e r o . 41 42 −f 43 F o r c e s o v e r w r i t i n g e x i s t i n g f i l e s 44 45 −r e m o v e 46 R e m o v e s a l l f i l e s p e r t a i n i n g t o t h i s s e r v i c e / v e r s i o n / i m p l e m e n t a i o n − b e c a r e f u l l ! 47 48 −t T E M P L A T E 49 N e w t e m p l a t e s c a n b e i n s t a l l e d . U s e o p t i o n −t l i s t t o l i s t a l l t e m p l a t e s 50 51 A U T H O R 52 P e t e r F i s c h e r H a l l i n , p f h @ c b s . d t u . dk , S e p t e m b e r 2008 53 54 S E E A L S O 55 / u s r / o p t / q u a q / 56 / u s r / o p t / w w w / cgi−b i n / C B S / s o a p / w s / q u a s i . c g i 57 58 A U T H O R 59 P e t e r H a l l i n 2008−09−15, p f h @ c b s . d t u . d k 173
BIBLIOGRAPHY Bibliography S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, & D. J. Lipman (1997). ‘Gapped blast <strong>and</strong> psi–blast: a new generation of prote<strong>in</strong> database searchprograms.’ Nucleic Acids Res 25:3389–402. B. F. Bauer, E. G. Kar, R. M. Elford, & W. M. Holmes (1988). ‘Sequence determ<strong>in</strong>ants for promoter strength <strong>in</strong> the leuv operon of Escherichia coli.’ Gene 63:123–34. J. Besemer, A. Lomsadze, & M. Borodovsky (2001). ‘GeneMarks: a self–tra<strong>in</strong><strong>in</strong>g method for prediction of gene starts <strong>in</strong> microbial genomes. Implications for f<strong>in</strong>d<strong>in</strong>g sequence motifs <strong>in</strong> regulatory regions.’ Nucleic Acids Res 29:2607–18. T. T. B<strong>in</strong>newies, P. F. Hall<strong>in</strong>, H.-H. Staerfeldt, & D. W. Ussery (2005). ‘Genome Update: proteome comparisons.’ Microbiology 151:1–4. T. T. B<strong>in</strong>newies, Y. Motro, P. F. Hall<strong>in</strong>, O. Lund, D. Dunn, T. La, D. J. Hampson, M. Bellgard, T. M. Wassenaar, & D. W. Ussery (2006). ‘Ten years of bacterial genome sequenc<strong>in</strong>g: comparative–genomics–baseddiscoveries.’ Funct Integr Genomics 6:165–85. E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigo, T. R. G<strong>in</strong>geras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clell<strong>and</strong>, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. J. Parker, P. J. Sabo, R. S<strong>and</strong>strom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Coll<strong>in</strong>s, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. S<strong>and</strong>el<strong>in</strong>, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sek<strong>in</strong>ger, J. Lagarde, J. F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermuller, J. Hertel, M. L<strong>in</strong>demeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Sr<strong>in</strong>ivasan, W.-K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, X. Zhang, P. Bickel, J. S. Mattick, P. Carn<strong>in</strong>ci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, 174
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Peter Fischer Hallin | 2009 Peter F
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Preface This Ph.D. thesis is writte
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thesis, the work is just being publ
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Paper VI [Lagesen K, Hallin P] 1 ,
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3.3.3 Refining E. coli and Shigella
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xviii 2.17 Pan- and core-genome plo
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Chapter 1 Introduction Introduction
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Chapter 2 Comparative Genomics 2.1
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Comparative Genomics the publicly a
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Comparative Genomics source CDS tot
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Listing 2.8: R code to generate a 2
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1st U C A G U 2nd position C A G 3r
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1st U C A G U 2nd position C A G 3r
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Escherichia coli strain K-12, subst
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Comparative Genomics
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3M 2.5M 3.5M 2.5M 2M 0M 2M 0.5M B.
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Streptococcus Escherichia Bacillus
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2.4 Summary Comparative Genomics Th
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‘ReSourCe is he best online submi
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up to a total of 41 different E. co
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Fig. 2 Genes (or segments) from eac
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Fig. 5 BLASTatlas of Clostridium bo
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166 literally millions of bacterial
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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180 reasons why organisms remain un
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182 A final problem has to do with
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184 Middendorf B, Hochhut B, Leipol
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2 O. N. Reva et al. Fig. 1. Genome
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phylogenies based on alternative ho
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25000 20000 15000 10000 5000 0 Pan
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Table 2 A selection of genes locate
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4318 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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