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1 : parrello 1.1 <?xml version="1.0" encoding="UTF-8"?>
2 :     <Database>
3 :     <Title>Similarity Block Database</Title>
4 :     <Entities>
5 :     <Entity name="Genome" keyType="name-string">
6 :     <Notes>A [i]genome[/i] contains the sequence data for a particular
7 : parrello 1.3 individual organism.</Notes>
8 :     <Fields>
9 :     <Field name="description" type="string">
10 :     <Notes>Brief description of this genome.</Notes>
11 :     </Field>
12 : parrello 1.4 <Field name="group-name" type="name-string">
13 :     <Notes>Name of this genome's close-strain group.</Notes>
14 :     </Field>
15 :    
16 : parrello 1.3 </Fields>
17 : parrello 1.4 <Indexes>
18 :     <Index>
19 :     <Notes>This index sorts the genomes by group so that
20 :     close strains are placed next to each other.</Notes>
21 :     <IndexFields>
22 :     <IndexField name="group-name" order="ascending" />
23 :     <IndexField name="id" order="ascending" />
24 :     </IndexFields>
25 :     </Index>
26 :     </Indexes>
27 : parrello 1.3 </Entity>
28 : parrello 1.2 <Entity name="Contig" keyType="key-string">
29 : parrello 1.1 <Notes>A [i]contig[/i] is a contiguous run of nucleotides. The contig's
30 : parrello 1.3 ID consists of the genome ID followed by a name that identifies
31 :     which contig this is for the parent genome. The individual components
32 :     are separated by a colon.</Notes>
33 : parrello 1.1 </Entity>
34 : parrello 1.4 <Entity name="GroupBlock" keyType="name-string">
35 : parrello 1.2 <Notes>A [i]group block[/i] is a set of similar genome regions.
36 : parrello 1.3 A group block can represent a gene or an inter-genic region.
37 :     The result is that every position in a contig belongs to exactly
38 :     one block, though some will belong to several.</Notes>
39 : parrello 1.1 <Fields>
40 :     <Field name="len" type="int">
41 : parrello 1.3 <Notes>Number of nucleotides in the regions belonging to
42 :     this block. This may include insertion markers ([b]-[/b]).</Notes>
43 :     </Field>
44 :     <Field name="pattern" type="text">
45 :     <Notes>A representation of the nucleotides in the group,
46 :     with question marks substituted for positions that are
47 :     not identical for all group members.</Notes>
48 :     </Field>
49 :     <Field name="variance" type="float">
50 :     <Notes>The proportion of nucleotides that vary between
51 :     regions in this group. For example, a value of 0 means all
52 :     regions are identical at every position. A value of
53 :     0.5 means all regions are identical at exactly half of
54 :     the positions. For a block length of 100, a value
55 :     of 0.03 means all regions are identical at every position
56 :     but 3. The variance does not indicate the degree
57 :     of dissimilarity, just how much of each region needs to be
58 :     examined for SNPs.</Notes>
59 :     </Field>
60 :     <Field name="snip-count" type="int">
61 :     <Notes>The number of positions at which the nucleotides
62 :     vary between regions in this group. The variance value
63 :     is this number divided by the block length.</Notes>
64 :     </Field>
65 :     <Field name="description" type="string">
66 :     <Notes>Descriptive name of this block. This will be
67 :     the gene name for gene blocks, and a generated
68 :     string for inter-genic blocks.</Notes>
69 :     </Field>
70 : parrello 1.1 </Fields>
71 :     </Entity>
72 : parrello 1.3 <Entity name="Region" keyType="name-string">
73 :     <Notes>A [i]region[/i] describes a location in a contig, and
74 :     essentially bridges the gap between blocks and contigs. Each
75 :     instance of this object corresponds to a single segment on
76 :     a contig. The key is the region's sprout-style location
77 :     string.</Notes>
78 : parrello 1.1 <Fields>
79 : parrello 1.3 <Field name="contigID" type="key-string">
80 :     <Notes>Name of the contig containing this region.</Notes>
81 :     </Field>
82 : parrello 1.1 <Field name="position" type="int">
83 : parrello 1.3 <Notes>Index (1-based) of the region's leftmost nucleotide
84 :     in the contig.</Notes>
85 :     </Field>
86 : parrello 1.1 <Field name="direction" type="char">
87 : parrello 1.3 <Notes>[b]+[/b] for a forward region, [b]-[/b] for a reverse
88 :     region.</Notes>
89 :     </Field>
90 :     <Field name="content" type="text">
91 :     <Notes>Nucleotide sequence of variance in this region
92 :     (upper case). For a forward region, this is the exact
93 :     content of each position of variance in the region.
94 :     For a reverse region, it is the complement in
95 :     reverse order.</Notes>
96 :     </Field>
97 :     <Field name="len" type="int">
98 :     <Notes>Length of this region. This may be slightly smaller
99 :     than the block length.</Notes>
100 :     </Field>
101 : parrello 1.5 <Field name="endpoint" type="int">
102 : parrello 1.3 <Notes>Index (1-based) of the region's rightmost nucleotide
103 :     in the contig.</Notes>
104 :     </Field>
105 :     <Field name="peg" type="name-string">
106 :     <Notes>PEG identifier for this block if it is a gene block,
107 :     or a string generated from the nearby PEGs if it is an
108 :     inter-genic block</Notes>
109 :     </Field>
110 : parrello 1.1 </Fields>
111 : parrello 1.3 <Indexes>
112 :     <Index>
113 :     <Notes>This index enables the application to find regions
114 :     that overlap a specific section of the contig. The index
115 :     can be used to find the first region whose end point is at
116 :     or follows the start of the section in question. Because
117 :     every nucleotide is in at most one region, this guarantees
118 :     that if any region overlaps the section, the region found
119 :     by the index will.</Notes>
120 :     <IndexFields>
121 : parrello 1.5 <IndexField name="endpoint" order="ascending" />
122 : parrello 1.3 </IndexFields>
123 :     </Index>
124 :     </Indexes>
125 :     </Entity>
126 : parrello 1.2 </Entities>
127 :     <Relationships>
128 :     <Relationship name="ContainsRegion" from="Contig" to="Region" arity="1M">
129 :     <Notes>This relationship connects contigs to the regions on
130 : parrello 1.3 them.</Notes>
131 :     <Fields>
132 : parrello 1.2 <Field name="position" type="int">
133 : parrello 1.3 <Notes>Index (1-based) of the region's leftmost nucleotide
134 :     in the contig.</Notes>
135 :     </Field>
136 :     <Field name="len" type="int">
137 :     <Notes>Length of this region. This may be slightly smaller
138 :     than the block length.</Notes>
139 :     </Field>
140 :     </Fields>
141 : parrello 1.2 <ToIndex>
142 : parrello 1.1 <Notes>This index enables the application to find all of the
143 : parrello 1.3 regions in a contig in the order they are present in the
144 :     contig.</Notes>
145 : parrello 1.1 <IndexFields>
146 :     <IndexField name="position" order="ascending" />
147 :     <IndexField name="len" order="descending" />
148 :     </IndexFields>
149 : parrello 1.2 </ToIndex>
150 : parrello 1.1 </Relationship>
151 : parrello 1.3 <Relationship name="IncludesRegion" from="GroupBlock" to="Region" arity="1M">
152 :     <Notes>This relationship connects a block to the regions it covers. Note
153 :     that since the ID of the region is its Sprout-style location string,
154 :     often it is not necessary to cross to the [b]Region[/b] table when
155 :     accessing this relationship.</Notes>
156 :     </Relationship>
157 : parrello 1.1 <Relationship name="HasInstanceOf" from="Genome" to="GroupBlock" arity="MM">
158 :     <Notes>This relationship connects a genome to the groups represented
159 : parrello 1.3 in its contigs. It provides a fast was to get an ordered list of
160 :     groups for a genome. The group lists for genomes can then be
161 :     merged to determine the common groups of a set of genomes.</Notes>
162 :     </Relationship>
163 :     <Relationship name="ConsistsOf" from="Genome" to="Contig" arity="1M">
164 :     <Notes>This relationship connects a genome to its contigs.</Notes>
165 : parrello 1.1 </Relationship>
166 :     </Relationships>
167 :     </Database>

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