FAQ
- What is Mbovis.org database?
- How do I submit a new spoligotype patterns?
- How do I cite Mbovis.org database?
- Which strains are included in Mbovis.org?
- Which nomenclature for spoligotypes is used in Mbovis.org?
- What is the binary (BIN) code?
- What is the hexadecimal (HEX) code?
- What is the octal (OCT) code?
What is Mbovis.org database?
Mbovis.org is a free database for the naming of spoligotype patterns from MTBC strains collected from animal species.
How do I submit a new spoligotype pattern?
Search for the spoligotype pattern in the database. If the pattern is not in the database, a message will be displayed asking for the e-mail to send you the instructions to submit the new patterns.
How do I cite Mbovis.org database?
Smith NH., Upton P. "Naming spoligotype patterns for the RD9-deleted lineage of the Mycobacterium tuberculosis complex; www.Mbovis.org". Infect Genet Evol. 12(4):873-6. 2012.
Which nomenclature for spoligotypes is used in Mbovis.org?
See this link for information about the spoligotype nomenclature.
What is the binary (BIN) code?
The spoligotype binary code uses the binary number system being 0 negative (spacer missing) and 1 positive (spacer present).
Example:
| Original pattern | |||||||||||||||||||||||||||||||||||||||||||
| Binary code | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Written as | 1001111101111110111101111111110000110100000 | ||||||||||||||||||||||||||||||||||||||||||
What is the hexadecimal (HEX) code?
Spoligotype patterns can be named using the HEX code system (Dale et al., 2001). The binary spoligotype pattern is divided up into 6 blocks each containing 7 or 8 spacers:
1 - 7, 8 - 14, 15 - 21, 22 - 28, 29 - 36 and 37- 43
The binary pattern of each blocks is converted to a two digit hexadecimal number. The 6X2 digit code is used as the name of the spoligotype pattern.
Example:
| Original pattern | |||||||||||||||||||||||||||||||||||||||||||
| Binary code | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Hex blocks | 1001111 | 1011111 | 1011110 | 1111111 | 11000011 | 0100000 | |||||||||||||||||||||||||||||||||||||
| Hex code | 4F | 5F | 5E | 7F | C3 | 20 | |||||||||||||||||||||||||||||||||||||
| Written as | 4F-5F-5E-7F-C3-20 | ||||||||||||||||||||||||||||||||||||||||||
What is the octal (OCT) code?
Spoligotype patterns can be named using the OCT code system (Dale et al., 2001). The pattern is read in groups of 3, as a 3-digit binary number can be read as a single digit octal number; in this way the binary series 000, 001, 010, 011, 100, 101, 110, 111 is read respectively as 0, 1, 2, 3, 4, 5, 6, 7. Following 14 groups of 3, the 43rd spacer is read on its own, simply as 0 or 1.
Example:
| Original pattern | |||||||||||||||||||||||||||||||||||||||||||
| Binary code | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Octal blocks | 100 | 111 | 110 | 111 | 111 | 011 | 110 | 111 | 111 | 111 | 000 | 011 | 010 | 000 | 0 | ||||||||||||||||||||||||||||
| Octal code | 4 | 7 | 6 | 7 | 7 | 3 | 6 | 7 | 7 | 7 | 0 | 3 | 2 | 0 | 0 | ||||||||||||||||||||||||||||
| Written as | 476773677703200 | ||||||||||||||||||||||||||||||||||||||||||
