Computational tools and Interoperability in Comparative ... - CBS

More documents

Recommendations

Info

4.4 The input web page of EPipe: Upper part defines sequence upload and alignment method, and lower part selects which modules / methods to run. When applicable, gene ontologies have been added to each feature and feature values (light green boxes). . . . . . . . . . . . . . . . . . . . . . . . 153 4.5 The mecA encoded protein (EEV85461) shows homology to PDB entry 1VQQ (Lim & Strynadka, 2002). Top panel shows the EPipe structure browser which allows for any 90 degrees rotating. Lower panel shows a post-processing of the PyMol script, generated by EPipe. . . . . . . . . . . 154 xix
Page 1 and 2: Peter Fischer Hallin | 2009 Peter F
Page 4: Preface This Ph.D. thesis is writte
Page 7 and 8: thesis, the work is just being publ
Page 9 and 10: ved at blive publiceret i Standards
Page 11 and 12: viii
Page 13 and 14: Paper VI [Lagesen K, Hallin P] 1 ,
Page 15 and 16: xii
Page 17 and 18: 3.3.3 Refining E. coli and Shigella
Page 19 and 20: xvi
Page 21: xviii 2.17 Pan- and core-genome plo
Page 25 and 26: organization to be answered. The de
Page 27 and 28: The genome annotation pipeline 2.2.
Page 29 and 30: The genome annotation pipeline AL11
Page 31 and 32: Genome Comparisons Right whisker en
Page 33 and 34: Genome Comparisons 12 10 12 Size di
Page 35 and 36: Genome Comparisons 12 TRNA_SCAN_COU
Page 37 and 38: Genome Comparisons N E D N E D N E
Page 39 and 40: Genome Comparisons Figure 2.8: Deam
Page 41 and 42: Genome Comparisons A.salmonicida LF
Page 43 and 44: Genome Comparisons by reading simpl
Page 45 and 46: Genome Comparisons Bacteria fix avg
Page 47 and 48: Genome Comparisons 0 1000 2000 3000
Page 49 and 50: Summary 26
Page 51 and 52: Instant insight: Reading the geneti
Page 53 and 54: HIGHLIGHT www.rsc.org/molecularbios
Page 55 and 56: each of the reference sequences is
Page 57 and 58: Table 2 A list of all strains and t
Page 59 and 60: Table 3 A list of all strains/sampl
Page 61 and 62: C. Herzberg, R. Martinez-Arias, R.
Page 63 and 64: Funct Integr Genomics (2006) 6: 165
Page 65 and 66: Fig. 1 Cumulative number of complet
Page 67 and 68: 3Fig. 2 a Phylogenetic tree of 287
Page 69 and 70: genomes which have been either comp
Page 71 and 72: are present in the first part of a
Page 73 and 74:
endonuclease. The occurrence of RM
Page 75 and 76:
Fig. 6 Genomic properties of Strept
Page 77 and 78:
3Fig. 7 Genome BLAST atlases. The o
Page 79 and 80:
consequences even though these orga
Page 81 and 82:
Goebel W, Gross R (2001) Intracellu
Page 83 and 84:
Schmidt H, Hensel M (2004) Pathogen
Page 85 and 86:
Environmental Microbiology (2007) d
Page 87 and 88:
Tümmler, 2004). Genomic regions te
Page 89 and 90:
T stretches (words of class 1) in A
Page 91 and 92:
short-chain n-alkanes by A. borkume
Page 93 and 94:
although in trees where both Pseudo
Page 95 and 96:
oligonucleotides from 2-mers to 8-m
Page 97 and 98:
Paper III: Global features of the A
Page 99 and 100:
Microb Ecol DOI 10.1007/s00248-009-
Page 101 and 102:
Origins of V. cholerae Table 1 Vibr
Page 103 and 104:
Origins of V. cholerae 68 68 93 64
Page 105 and 106:
Origins of V. cholerae Figure 4 BLA
Page 107 and 108:
Origins of V. cholerae When the fir
Page 109 and 110:
Origins of V. cholerae Table 2 (con
Page 111 and 112:
Origins of V. cholerae 36. Pinhassi
Page 113 and 114:
74 Tools for Comparison of Bacteria
Page 115 and 116:
. Table 1 Methods for comparison of
Page 117 and 118:
eplication tends to be more GC rich
Page 119 and 120:
Tools for Comparison of Bacterial G
Page 121 and 122:
Basic Local Alignment Search Tool,
Page 123 and 124:
Methanosphaera stadtmanae DSM 3091
Page 125 and 126:
8 Gene Synteny and Genome Islands A
Page 127 and 128:
acteria reveals a complex set of gr
Page 129 and 130:
Conservation of regulatory elements
Page 131 and 132:
Page 133 and 134:
Page 135 and 136:
Page 137 and 138:
DNA melting and SIDD energy Z−sco
Page 139 and 140:
DNA melting and SIDD energy P1 -10
Page 141 and 142:
Visualizing sequencing quality usin
Page 143 and 144:
Summary 120
Page 145 and 146:
3100-3108 Nucleic Acids Research, 2
Page 147 and 148:
3102 Nucleic Acids Research, 2007,
Page 149 and 150:
Page 151 and 152:
Page 153 and 154:
Page 155 and 156:
Standards in Genomic Sciences (2009
Page 157 and 158:
GeneWiz browser Figure 1 | Mapping
Page 159 and 160:
GeneWiz browser nearly instantly wh
Page 161 and 162:
GeneWiz browser Table 3 Sequencing
Page 163 and 164:
GeneWiz browser The SIDD atlas: Ann
Page 165 and 166:
GeneWiz browser assembly. Genome Bi
Page 167 and 168:
Paper VII: GeneWiz browser: An Inte
Page 169 and 170:
Interoperability Figure 4.1: Screen
Page 171 and 172:
EMBRACE: An EU initiative for enhan
Page 173 and 174:
EMBRACE: An EU initiative for enhan
Page 175 and 176:
ENCODE pipeline: applying Web Servi
Page 177 and 178:
ENCODE pipeline: applying Web Servi
Page 179 and 180:
gramming environment which scales s
Page 181 and 182:
Workshops and meetings A.1.7 EMBRAC
Page 183 and 184:
Danmarks Tekniske Universitet AFI,
Page 185 and 186:
Page 187 and 188:
Page 189 and 190:
Appendix D Appendix: Software D.1 f
Page 191 and 192:
BLASTatlas configurations 47 B a c
Page 193 and 194:
iscan source code 13 i f ( d e f i
Page 195 and 196:
quasi mktemp manual 201 r e t u r n
Page 197 and 198:
BIBLIOGRAPHY Bibliography S. F. Alt
Page 199 and 200:
BIBLIOGRAPHY Hooton, E. R. Mardis,
Page 201 and 202:
BIBLIOGRAPHY A. Nakabachi, A. Yamas
Page 203:
BIBLIOGRAPHY R. A. Welch, V. Burlan
show all

Computational tools and Interoperability in Comparative ... - CBS

Create successful ePaper yourself

Delete template?

Save as template?