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Database conventions

Text Search

In order to start a test search, you must first select one interested field from the cascade menu above. There are four options:
General information includes the characteristics and disease caused by the pathogens, as well as the general information of each genus.
Virulence factors include the name, full name, characteristics, structure, function and mechanism of each VFs.
Pathogenicity islands include the name, full name, locus feature, phenotype and remark information of each PAIs.
Gene refers the name and product description of each VFs related gene (includes those genes located in PAIs).
Comparative pathogenomics refers the names of all VFs and related genes involved in the comparative pathogenomics datasets.

Then, input the query texts in the entry box and click the 'Search' button below. You can input either a single keyword or multiple alternative keywords separated by blanks. Note that here alternative means any keyword match will be reported to the users by default.
If you do need to search the database by complex phrases that contain blanks, please enclose them into double quotation marks ("). For example, in order to use 'M protein' as one of the keywords to search the database, you should input "M protein" instead of just input M protein.

Please also pay attention to the following search conventions:
By default, the search engine is case insensitive.
The search engine only report results with whole words matches to the given keywords. For example, the word 'pathogenicity' will NOT treat as good match to the keyword 'pathogenic' by the search engine. Hence, you might need to try more keywords sometimes.
In order to avoid numerous stochastic matches, those input keywords with length less than 3 characters will be automatically ignored by the search engine.
Any non-words special characters, such as semicolon, are treated as invalid by the search engine and will be removed automatically.


Figure legends of circular and linear maps

In circular maps, each ORF was represented as a small colored triangle around the circle. Location in outer circle (red) and inner circle (blue) represent genes located in leading and lagging strands, respectively.

In linear maps, the meanings of all types of symbols are listed below:
Symbols representations
 
Symbols
Explain
ORF with the arrow direction indicates its coding strand, and the gene name is displayed above the ruler. There is a cross over the arrow if it's a pseudogene.
tRNA gene and its type is displayed above.
IS element and its type is displayed below.
 

The ORFs in linear maps were colored by its function category in COGs:
Color representations
 
Code  
Color
  Function
  Information storage and processing
J
    Translation, ribosomal structure and biogenesis
 
A
    RNA processing and modification
 
K
    Transcription
 
L
    Replication, recombination and repair
 
B
    Chromatin structure and dynamics
 
  Cellular processes and signaling
D
    Cell cycle control, cell division and chromosome partitioning
 
V
    Defense mechanisms
 
T
    Signal transduction mechanisms
 
O
    Posttranslational modification, protein turnover, chaperones
 
M
    Cell wall/membrane/envelope biogenesis
 
N
    Cell motility
 
W
    Extracellular structures
 
U
    Intracellular trafficking, secretion, and vesicular transport
 
  Metabolism
C
    Energy production and conversion
 
G
    Carbohydrate transport and metabolism
 
E
    Amino acid transport and metabolism
 
F
    Nucleotide transport and metabolism
 
H
    Coenzyme transport and metabolism
 
I
    Lipid transport and metabolism
 
P
    Inorganic ion transport and metabolism
 
Q
    Secondary metabolites biosynthesis, transport and catabolism
 
  Poorly characterized
R
    General function prediction only
 
S
    Function unknown
 
Table reproduced from COG database