User Guide of VNTRDB

1
User Guide of VNTRDB

• For molecular typing of bacteria belonged to a
  same genus

2
? Press here to start query
3
? Select certain bacterial genus for typing
4
View query results and select candidate loci for
molecular typing
5
? Click on the link to reorganize the order of
query results by length polymorphism level
?or the order of pattern size, of match and raw
length
View query results and select candidate loci for
molecular typing
6
Priority for locus selection Length polymorphism
level Raw length of tandem repeat, Size of
consensus pattern Copy difference Match of
consensus pattern
? Link to the visualization tool
?Click on here to view the tandem repeat and its
flanking sequences
View locus details and design primers for
molecular typing
7
For solving copy and length uncertainty
8
Multiple alignment of the flanking
sequences, then use Primer3 for primer design and
use BLAST for checking identity of primers
among all known bacterial genomes
9
? Reselect the bacterial species for typing
10
User Guide of VNTRDB

• Freely browse this database and set parameters by
  self

11
? Select certain bacterial genus for typing
12
? Reselect the bacterial species for typing
13
? Check this box for setting more parameters
View query results and select candidate loci for
molecular typing
14
Reset parameters and select candidate loci for
molecular typing
15
Reset parameters and select candidate loci for
molecular typing
16
User Guide of VNTRDB

• For identification of a specific genus of bacteria

17
? Check for identify inter-genus unique TRs
?Select a bacterial genus and submit the job
18
?Click on the link to reorganize the order of raw
length of repeat
?or the order of pattern size and of match
View query results and select candidate loci for
experimental identification
19
Get help
? Click on here to view the tandem repeat and its
flanking sequences
Priority for selecting loci Raw length of tandem
repeat, Size of consensus pattern Match of
consensus pattern
View locus details and design primers for
experimental identification
20
Blast the flanking sequences against bacterial
genomes, then design primers using Primer3
21
User Guide of VNTRDB

• For identification of certain species of bacterium

22
? Press here to start query
23
? Check for identify inter-genus unique TRs
?Select a bacterial genus
24
?Select a bacterial genus and submit the job
25
?Click on the link to reorganize the order of raw
length of repeat
? or the order of pattern size and of match
View query results and select candidate loci for
experimental identification
26
Get help
? Click on here to view the tandem repeat and its
flanking sequences
Priority for selecting loci Raw length of tandem
repeat, Size of consensus pattern Match of
consensus pattern
View locus details and design primers for
experimental identification
27
Blast the flanking sequences against bacterial
genomes, then design primers using Primer3
28
User Guide of VNTRDB

• To clarify if there is any correlation between
  VNTRs and specific features (e.g., pathogenicity)
  in similar bacteria genera or species

29

• Check this for typing the different
• bacterial species with similar features

? Select certain group of bacteria for typing
30
?Click on the link to reorganize the order of
query results
View query results and select candidate loci for
molecular typing
31
Priority for selecting loci Length polymorphism
level Raw length of tandem repeat, Size of
consensus pattern Copy difference Match of
consensus pattern
? Link to visualization tool
? Click on here to view the tandem repeat and its
flanking sequences
View locus details and design primers for
molecular typing
32
For solving copy and length uncertainty
33
Multiple alignment of the flanking
sequences, then use Primer3 for primer design and
use BLAST for checking identity of primers
among all known bacterial genomes