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D.2 Sample output from queryGenomes As output from listing 2.3. Appendix: Software 1 #kingdom phyla pid organism genbank r e f s e q segment c o l o r ATCONTENT NGENES 2 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 7 9 N C _ 0 1 1 3 1 2 C h r o m o s o m e 1 f f d d 4 4 0 . 6 0 7 7 3069 3 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 8 0 N C _ 0 1 1 3 1 3 C h r o m o s o m e 2 f f d d 4 4 0 . 6 1 7 6 1105 4 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 8 2 N C _ 0 1 1 3 1 4 P l a s m i d p V S A L 3 2 0 f f d d 4 4 0 . 6 2 7 1 32 5 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 8 1 N C _ 0 1 1 3 1 1 P l a s m i d p V S A L 8 4 0 f f d d 4 4 0 . 5 9 9 3 72 6 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 8 3 N C _ 0 1 1 3 1 5 P l a s m i d p V A L 4 3 f f d d 4 4 0 . 6 1 9 3 7 B a c t e r i a G a m m a p r o t e o b a c t e r i a 30703 A l i i v i b r i o s a l m o n i c i d a L F I 1 2 3 8 F M 1 7 8 3 8 4 N C _ 0 1 1 3 1 6 P l a s m i d p V S A L 4 3 f f d d 4 4 0 . 6 4 3 9 3 8 B a c t e r i a D e l t a p r o t e o b a c t e r i a 9637 B d e l l o v i b r i o b a c t e r i o v o r u s H D 1 0 0 B X 8 4 2 6 0 1 N C _ 0 0 5 3 6 3 C h r o m o s o m e f f d d 4 4 0 . 4 9 3 5 3583 9 B a c t e r i a G a m m a p r o t e o b a c t e r i a 28329 C e l l v i b r i o j a p o n i c u s U e d a 1 0 7 C P 0 0 0 9 3 4 N C _ 0 1 0 9 9 5 C h r o m o s o m e f f d d 4 4 0 . 4 8 0 1 3754 10 B a c t e r i a B a c t e r o i d e t e s / C h l o r o b i 12607 C h l o r o b i u m p h a e o v i b r i o i d e s D S M 265 C P 0 0 0 6 0 7 N C _ 0 0 9 3 3 7 C h r o m o s o m e f f b b 5 5 0 . 4 7 0 1 1753 11 B a c t e r i a D e l t a p r o t e o b a c t e r i a 29493 D e s u l f o v i b r i o d e s u l f u r i c a n s s u b s p . d e s u l f u r i c a n s s t r . A T C C 27774 C P 0 0 1 3 5 8 N C _ 0 1 1 8 8 3 C h r o m o s o m e f f d d 4 4 0 . 4 1 9 3 2356 12 B a c t e r i a D e l t a p r o t e o b a c t e r i a 329 D e s u l f o v i b r i o d e s u l f u r i c a n s s u b s p . d e s u l f u r i c a n s s t r . G 2 0 C P 0 0 0 1 1 2 N C _ 0 0 7 5 1 9 C h r o m o s o m e f f d d 4 4 0 . 4 2 1 6 3775 13 B a c t e r i a D e l t a p r o t e o b a c t e r i a 32105 D e s u l f o v i b r i o m a g n e t i c u s RS −1 A P 0 1 0 9 0 6 N C _ 0 1 2 7 9 5 P l a s m i d p D M C 2 f f d d 4 4 0 . 6 2 8 3 10 14 B a c t e r i a D e l t a p r o t e o b a c t e r i a 32105 D e s u l f o v i b r i o m a g n e t i c u s RS −1 A P 0 1 0 9 0 4 N C _ 0 1 2 7 9 6 C h r o m o s o m e f f d d 4 4 0 . 3 7 2 3 4629 15 B a c t e r i a D e l t a p r o t e o b a c t e r i a 32105 D e s u l f o v i b r i o m a g n e t i c u s RS −1 A P 0 1 0 9 0 5 N C _ 0 1 2 7 9 7 P l a s m i d p D M C 1 f f d d 4 4 0 . 4 1 9 7 65 16 B a c t e r i a D e l t a p r o t e o b a c t e r i a 29541 D e s u l f o v i b r i o s a l e x i g e n s D S M 2638 C P 0 0 1 6 4 9 N C _ 0 1 2 8 8 1 C h r o m o s o m e f f d d 4 4 0 . 5 2 9 1 3807 17 B a c t e r i a D e l t a p r o t e o b a c t e r i a 17227 D e s u l f o v i b r i o v u l g a r i s D P 4 C P 0 0 0 5 2 8 N C _ 0 0 8 7 4 1 P l a s m i d p D V U L 0 1 f f d d 4 4 0 . 3 4 3 1 150 18 B a c t e r i a D e l t a p r o t e o b a c t e r i a 17227 D e s u l f o v i b r i o v u l g a r i s D P 4 C P 0 0 0 5 2 7 N C _ 0 0 8 7 5 1 C h r o m o s o m e f f d d 4 4 0 . 3 6 9 9 2941 19 B a c t e r i a D e l t a p r o t e o b a c t e r i a 27731 D e s u l f o v i b r i o v u l g a r i s s t r . M i y a z a k i F C P 0 0 1 1 9 7 N C _ 0 1 1 7 6 9 C h r o m o s o m e f f d d 4 4 0 . 3 2 8 9 3180 20 B a c t e r i a D e l t a p r o t e o b a c t e r i a 51 D e s u l f o v i b r i o v u l g a r i s s t r . H i l d e n b o r o u g h A E 0 1 7 2 8 5 N C _ 0 0 2 9 3 7 C h r o m o s o m e f f d d 4 4 0 . 3 6 8 6 3379 21 B a c t e r i a D e l t a p r o t e o b a c t e r i a 51 D e s u l f o v i b r i o v u l g a r i s s t r . H i l d e n b o r o u g h A E 0 1 7 2 8 6 N C _ 0 0 5 8 6 3 M e g a p l a s m i d f f d d 4 4 0 . 3 4 3 2 152 22 B a c t e r i a O t h e r B a c t e r i a 30733 T h e r m o d e s u l f o v i b r i o y e l l o w s t o n i i D S M 11347 C P 0 0 1 1 4 7 N C _ 0 1 1 2 9 6 C h r o m o s o m e 888888 0 . 6 5 8 7 2033 23 B a c t e r i a G a m m a p r o t e o b a c t e r i a 29177 T h i o a l k a l i v i b r i o s p . HL−E b G R 7 C P 0 0 1 3 3 9 N C _ 0 1 1 9 0 1 C h r o m o s o m e f f d d 4 4 0 . 3 4 9 4 3283 24 B a c t e r i a G a m m a p r o t e o b a c t e r i a 32851 V i b r i o c h o l e r a e M66 −2 C P 0 0 1 2 3 3 N C _ 0 1 2 5 7 8 C h r o m o s o m e I f f d d 4 4 0 . 5 2 1 7 2650 25 B a c t e r i a G a m m a p r o t e o b a c t e r i a 32851 V i b r i o c h o l e r a e M66 −2 C P 0 0 1 2 3 4 N C _ 0 1 2 5 8 0 C h r o m o s o m e I I f f d d 4 4 0 . 5 2 9 6 1043 26 B a c t e r i a G a m m a p r o t e o b a c t e r i a 33555 V i b r i o c h o l e r a e MJ −1236 C P 0 0 1 4 8 5 N C _ 0 1 2 6 6 8 C h r o m o s o m e 1 f f d d 4 4 0 . 5 2 4 8 2770 27 B a c t e r i a G a m m a p r o t e o b a c t e r i a 33555 V i b r i o c h o l e r a e MJ −1236 C P 0 0 1 4 8 6 N C _ 0 1 2 6 6 7 C h r o m o s o m e 2 f f d d 4 4 0 . 5 3 2 5 1004 28 B a c t e r i a G a m m a p r o t e o b a c t e r i a 36 V i b r i o c h o l e r a e O 1 b i o v a r E l T o r s t r . N 1 6 9 6 1 A E 0 0 3 8 5 2 N C _ 0 0 2 5 0 5 C h r o m o s o m e I f f d d 4 4 0 . 5 2 3 2736 29 B a c t e r i a G a m m a p r o t e o b a c t e r i a 36 V i b r i o c h o l e r a e O 1 b i o v a r E l T o r s t r . N 1 6 9 6 1 A E 0 0 3 8 5 3 N C _ 0 0 2 5 0 6 C h r o m o s o m e I I f f d d 4 4 0 . 5 3 0 9 1092 30 B a c t e r i a G a m m a p r o t e o b a c t e r i a 15667 V i b r i o c h o l e r a e O 3 9 5 C P 0 0 0 6 2 6 N C _ 0 0 9 4 5 6 C h r o m o s o m e 1 f f d d 4 4 0 . 5 3 1 2 1133 31 B a c t e r i a G a m m a p r o t e o b a c t e r i a 15667 V i b r i o c h o l e r a e O 3 9 5 C P 0 0 0 6 2 7 N C _ 0 0 9 4 5 7 C h r o m o s o m e 2 f f d d 4 4 0 . 5 2 2 2 2742 32 B a c t e r i a G a m m a p r o t e o b a c t e r i a 12986 V i b r i o f i s c h e r i E S 1 1 4 C P 0 0 0 0 2 0 N C _ 0 0 6 8 4 0 C h r o m o s o m e I f f d d 4 4 0 . 6 1 0 4 2575 33 B a c t e r i a G a m m a p r o t e o b a c t e r i a 12986 V i b r i o f i s c h e r i E S 1 1 4 C P 0 0 0 0 2 1 N C _ 0 0 6 8 4 1 C h r o m o s o m e I I f f d d 4 4 0 . 6 2 9 8 1172 34 B a c t e r i a G a m m a p r o t e o b a c t e r i a 12986 V i b r i o f i s c h e r i E S 1 1 4 C P 0 0 0 0 2 2 N C _ 0 0 6 8 4 2 P l a s m i d p E S 1 0 0 f f d d 4 4 0 . 6 1 5 8 55 35 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19393 V i b r i o f i s c h e r i M J 1 1 C P 0 0 1 1 3 3 N C _ 0 1 1 1 8 6 C h r o m o s o m e I I f f d d 4 4 0 . 6 2 7 5 1254 36 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19393 V i b r i o f i s c h e r i M J 1 1 C P 0 0 1 1 3 4 N C _ 0 1 1 1 8 5 P l a s m i d p M J 1 0 0 f f d d 4 4 0 . 6 5 2 195 37 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19393 V i b r i o f i s c h e r i M J 1 1 C P 0 0 1 1 3 9 N C _ 0 1 1 1 8 4 C h r o m o s o m e I f f d d 4 4 0 . 6 1 1 2 2590 38 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19857 V i b r i o h a r v e y i A T C C BAA −1116 C P 0 0 0 7 9 1 N C _ 0 0 9 7 7 7 P l a s m i d p V I B H A R f f d d 4 4 0 . 5 6 2 1 120 39 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19857 V i b r i o h a r v e y i A T C C BAA −1116 C P 0 0 0 7 8 9 N C _ 0 0 9 7 8 3 C h r o m o s o m e I f f d d 4 4 0 . 5 4 4 5 3570 40 B a c t e r i a G a m m a p r o t e o b a c t e r i a 19857 V i b r i o h a r v e y i A T C C BAA −1116 C P 0 0 0 7 9 0 N C _ 0 0 9 7 8 4 C h r o m o s o m e I I f f d d 4 4 0 . 5 4 7 3 2374 41 B a c t e r i a G a m m a p r o t e o b a c t e r i a 360 V i b r i o p a r a h a e m o l y t i c u s R I M D 2210633 B A 0 0 0 0 3 1 N C _ 0 0 4 6 0 3 C h r o m o s o m e I f f d d 4 4 0 . 5 4 6 1 3080 42 B a c t e r i a G a m m a p r o t e o b a c t e r i a 360 V i b r i o p a r a h a e m o l y t i c u s R I M D 2210633 B A 0 0 0 0 3 2 N C _ 0 0 4 6 0 5 C h r o m o s o m e I I f f d d 4 4 0 . 5 4 6 5 1752 43 B a c t e r i a G a m m a p r o t e o b a c t e r i a 32815 V i b r i o s p l e n d i d u s L G P 3 2 F M 9 5 4 9 7 3 N C _ 0 1 1 7 4 4 C h r o m o s o m e 2 f f d d 4 4 0 . 5 6 3 6 1486 44 B a c t e r i a G a m m a p r o t e o b a c t e r i a 32815 V i b r i o s p l e n d i d u s L G P 3 2 F M 9 5 4 9 7 2 N C _ 0 1 1 7 5 3 C h r o m o s o m e 1 f f d d 4 4 0 . 5 5 9 6 2950 45 B a c t e r i a G a m m a p r o t e o b a c t e r i a 349 V i b r i o v u l n i f i c u s C M C P 6 A E 0 1 6 7 9 5 N C _ 0 0 4 4 5 9 C h r o m o s o m e I f f d d 4 4 0 . 5 3 5 5 2973 46 B a c t e r i a G a m m a p r o t e o b a c t e r i a 349 V i b r i o v u l n i f i c u s C M C P 6 A E 0 1 6 7 9 6 N C _ 0 0 4 4 6 0 C h r o m o s o m e I I f f d d 4 4 0 . 5 2 8 8 1565 167
BLASTatlas configurations 47 B a c t e r i a G a m m a p r o t e o b a c t e r i a 1430 V i b r i o v u l n i f i c u s Y J 0 1 6 B A 0 0 0 0 3 7 N C _ 0 0 5 1 3 9 C h r o m o s o m e I f f d d 4 4 0 . 5 3 5 9 3262 48 B a c t e r i a G a m m a p r o t e o b a c t e r i a 1430 V i b r i o v u l n i f i c u s Y J 0 1 6 B A 0 0 0 0 3 8 N C _ 0 0 5 1 4 0 C h r o m o s o m e I I f f d d 4 4 0 . 5 2 7 9 1697 49 B a c t e r i a G a m m a p r o t e o b a c t e r i a 1430 V i b r i o v u l n i f i c u s Y J 0 1 6 A P 0 0 5 3 5 2 N C _ 0 0 5 1 2 8 P l a s m i d p Y J 0 1 6 f f d d 4 4 0 . 5 5 0 7 69 D.3 BLASTatlas configurations D.3.1 file blast.cfg 1 l e g e n d : B . a m b i f a r i a A M M D 2 p r o g r a m : b l a s t p 3 c o l o r : 1 0 1 0 1 0 _ 0 2 0 0 0 2 4 r a n g e : 0 . 0 , 0 . 8 5 s o u r c e : f i l e s / 1 3 4 9 0 . f s a 6 7 l e g e n d : B . a m b i f a r i a M C 4 0 −6 8 p r o g r a m : b l a s t p 9 c o l o r : 1 0 1 0 1 0 _ 0 2 0 0 0 2 10 r a n g e : 0 . 0 , 0 . 8 11 s o u r c e : f i l e s / 1 7 4 1 1 . f s a 12 13 l e g e n d : B . c e n o c e p a c i a A U 1054 14 p r o g r a m : b l a s t p 15 c o l o r : 1 0 1 0 1 0 _ 0 8 0 0 0 0 16 r a n g e : 0 . 0 , 0 . 8 17 s o u r c e : f i l e s / 1 3 9 1 9 . f s a 18 19 l e g e n d : B . c e n o c e p a c i a H I 2 4 2 4 20 p r o g r a m : b l a s t p 21 c o l o r : 1 0 1 0 1 0 _ 0 8 0 0 0 0 22 r a n g e : 0 . 0 , 0 . 8 23 s o u r c e : f i l e s / 1 3 9 1 8 . f s a 24 25 l e g e n d : B . c e n o c e p a c i a J 2 3 1 5 26 p r o g r a m : b l a s t p 27 c o l o r : 1 0 1 0 1 0 _ 0 8 0 0 0 0 28 r a n g e : 0 . 0 , 0 . 8 29 s o u r c e : f i l e s / 3 3 9 . f s a 30 31 l e g e n d : B . c e n o c e p a c i a MC0 −3 32 p r o g r a m : b l a s t p 33 c o l o r : 1 0 1 0 1 0 _ 0 8 0 0 0 0 34 r a n g e : 0 . 0 , 0 . 8 35 s o u r c e : f i l e s / 1 7 9 2 9 . f s a 36 37 l e g e n d : B . g l u m a e B G R 1 38 p r o g r a m : b l a s t p 39 c o l o r : 1 0 1 0 1 0 _ 0 5 0 5 0 5 40 r a n g e : 0 . 0 , 0 . 8 41 s o u r c e : f i l e s / 3 3 9 0 1 . f s a 42 43 . . . . . . D.3.2 file custom.cfg 1 2 l e g e n d : S I D D @ −0.035 3 c o l o r : 0 0 0 0 1 0 _ 1 0 1 0 1 0 4 r a n g e : 9 : 1 0 5 b o x f i l t e r : 5 0 0 0 6 s o u r c e : g u n z i p −c B X 5 7 1 9 6 6 −57 a 2 f 2 c 2 e 1 1 c a 0 d d 8 c d 7 4 4 9 3 d 6 6 7 d 4 d 6 −3173005. s i d d −−0.035−c−10−c . o u t . g z | c u t −f 4 | D.4 BLASTmatrix example This Perl script constructs an XML configuration file by looking up the Genome Atlas Database through MySQL. It queries for all Campylobacter strains currently available. 1 #! / u s r / bin / p e r l 2 u s e s t r i c t ; 3 4 m y $ S A C O _ E X T R A C T = " / u s r / c b s / b i o / b i n / l i n u x 6 4 / s a c o _ e x t r a c t " ; 5 m y %c o l o r s = ( l a r i => ’ 0 , 1 0 4 , 1 3 9 ’ , j e j u n i => ’ 0 , 1 3 9 , 6 9 ’ , h o m i n i s => ’ 66 , 66 , 1 1 1 ’ , f e t u s => ’ 1 3 9 , 1 0 1 , 8 ’ , c u r v u s=>’ 1 4 0 , 23 , 2 3 ’ , c o n c i s u s=>’ 2 0 5 , 1 7 3 , 0 ’ ) ; 6 7 m y $ s o u r c e s = " " ; # h o l d s the s o u r c e s p a r t o f the c o n f i g u r a t i o n − r e p l a c e i n t o DATA s e c t i o n 8 9 o p e n O R G A N I S M , " m y s q l - N - B - e \ " s e l e c t pid , o r g a n i s m _ n a m e f r o m g e n o m e a t l a s 3 _ c u r . g e n b a n k _ c o m p l e t e _ p r j w h e r e o r g a n i s m _ n a m e l i k e ’ c a m p y l o b a c t e r % ’ o r d e r b y o r g a n i s m _ n a m e \ " | " o r d i e $ ! ; 10 w h i l e (< O R G A N I S M >) { 11 c h o m p ; 12 m y ( $ p i d , $ o r g a n i s m _ n a m e ) = s p l i t /\ t / ; 168
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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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ved at blive publiceret i Standards
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viii
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Paper VI [Lagesen K, Hallin P] 1 ,
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xii
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3.3.3 Refining E. coli and Shigella
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xvi
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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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Comparative Genomics 1 mysql -N -B
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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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Comparative Genomics 2.5 Instant in
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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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different applications, such as ide
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1 Comparative Genomics 2.7 Paper II
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166 literally millions of bacterial
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168
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170 resistance genes on mobile gene
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172 involved in generating diversit
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174 recipient DNA. A feature observ
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176 Fig. 5 Genome length distributi
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178
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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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1 Comparative Genomics 2.8 Paper II
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2 O. N. Reva et al. Fig. 1. Genome
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4 O. N. Reva et al. decrease of the
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6 O. N. Reva et al. of which are kn
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8 O. N. Reva et al. compiled into a
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10 O. N. Reva et al. encoded by a c
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12 O. N. Reva et al. systems and ef
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1 2.9 Paper IV: The origins of Vibr
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phylogenies based on alternative ho
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Figure 1 Phylogenetic tree of the 1
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25000 20000 15000 10000 5000 0 Pan
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Gap F 2M 2.5M Gap E 875k 750k 625k
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Table 2 A selection of genes locate
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Open Access This article is distrib
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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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tuB murI Fis III Fis II Fis I UP -3
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Bits 2.0 1.5 1.0 0.5 0.0 Bits 2.0 1
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RNA operons and promoter analysis O
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Bits 2.0 1.5 1.0 0.5 0.0 Bits T A T
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Code Meaning Example C Coding CCCCC
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Page 142 and 143: P2 -10 -35 UP P1 -10 -35 UP FIS FIS
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Page 146 and 147: Using HMMs also simplifies the use
Page 148 and 149: Information content Information con
Page 150 and 151: of the annotation. Some of the majo
Page 152 and 153: where match states stop around 10 c
Page 154 and 155: 1 rRNA operons and promoter analysi
Page 156 and 157: synthesis in flow cells to simultan
Page 158 and 159: Read absence. A boolean where ‘on
Page 160 and 161: Hallin, et al. Figure 4 | The dataf
Page 162 and 163: Genome homology: Comparing multiple
Page 164 and 165: ing platform-‐independent Java
Page 166 and 167: 34. Wang H, Noordewier M, Benham CJ
Page 168 and 169: Chapter 4 Web Services and Interope
Page 170 and 171: Web Services and Interoperability i
Page 178 and 179: Chapter 5 Conclusion and perspectiv
Page 180 and 181: Appendix A Appendix: Workshops, tea
Page 182 and 183: Appendix B Appendix: Ph.D. study pl
Page 184 and 185: Danmarks Tekniske Universitet AFI,
Page 186 and 187: Danmarks Tekniske Universitet AFI,
Page 188 and 189: Appendix C Appendix: Courses C.1 Gl
Page 192 and 193: Appendix: Software 13 w a r n " $ o
Page 194 and 195: Appendix: Software 109 m y ( $ m i
Page 196 and 197: Appendix: Software 25 [ ] A l t e r
Page 198 and 199: BIBLIOGRAPHY J. Rogers, P. F. Stadl
Page 200 and 201: BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
Page 202 and 203: BIBLIOGRAPHY Velicer, F.-J. Vorholt
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