Tandyman Search Tips!
The following search criteria are recommended, as the indicated unit sizes and number of units have not only appeared to be biologically relevant in the literature but these individual searches will provide you relevant data quickly:
| Repeat Unit | Number of Units for a Repeat | Relevant Reference 1 |
|---|---|---|
| Mononucleotide | 7-9 2 | Jennings et al., 1999 |
| Dinucleotide | 5-6 | Peck et al., 1999 |
| Trinucleotide | 8+ | Parniewski et al., 2000 |
| Tetranucleotide | 3 | Hosking et al., 1999 |
| Pentanucleotide and bigger | 2 | Jackson et al., 1997 |
1: For more references, please see the publication, Cleland, C.A., R.W. Leach and C. Forst. 2000. Submitted to NAR.
2: The number of units per repeat depend on the AT content of a genome. If the GC to AT ratio is 1:1, the lower limit is reasonable. If the GC to AT ratio is skewed, the upper limit is reasonable.
If you use Tandyman in your analyses, please use this as a reference: Cleland, C.A., R.W. Leach and C. Forst. 2000. Submitted to Nucleic Acids Res.
References
Hosking,S.L., Craig,J.E., and High,N.J. 1999. Phase variation of lic1A, lic2A and lic3A in colonization of the nasopharynx, bloodstream and cerebrospinal fluid by Haemophilus influenzae type b. Microbiology 145(Pt 11):3005-11.
Jackson,P.J., Walthers,E.A., Kalif,A.S., Richmond,K.L., Adair,D.M., Hill,K.K., Kuske,C.R., Andersen,G.L., Wilson,K.H., Hugh-Jones,M., and Keim,P. (1997). Characterization of the variable number tandem repeats in vrrA from different Bacillus anthracis isolates. Applied and Environmental Microbiology 63:1400-1405.
Jennings,M.P., Srikhanta,Y.N., Moxon,E.R., Kramer,M., Poolman,J.T., Kuipers,B., and van der Ley,P. (1999). The genetic basis of the phase variation repertoire of lipopolysaccharide immunotypes in Neisseria meningitidis. Microbiology 145: 3013-3021.
Parniewski,P., Jaworski,A., Wells,R.D., and Bowater,R.P. 2000. Length of CTG.CAG repeats determines the influence of mismatch repair on genetic instability. J Mol Biol 299(4):865-74.
Peck,B., Ortkamp,M., Diehl,K.D., Hundt,E., and Knapp,B. (1999). Conservation, localization and expression of HopZ, a protein involved in adhesion of Helicobacter pylori. Nucleic Acids Res 27:3325-3333.
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