XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences

Table 1 User-defined parameters

Definition	Default Value
Minimum character identity i	0.7 for proteins 0.8 for nucleotides
Minimum consensus matching I	0.8
Minimum copy number MinC	3
Minimum period MinP	3 for proteins 10 for nucleotides
Maximum period MaxP	Half of input sequence length
Maximum consecutive gaps g (see Appendix)	3
Maximum indel error (see Appendix)	0.5

Shown in this table are seven important user-adjustable parameters used by XSTREAM. These parameters function to limit the extent of TR degeneracy as well as to restrict the TR period and copy number of reported TRs. Default parameter values were empirically chosen to preferentially identify and model long degenerate repeat regions rather than shorter repetitive regions with higher sequence identity (e.g., where I = 1.0 and g = 0). We acknowledge that alternative architectures may exist for some complex repetitive domains. By including these and additional modifiable parameters, XSTREAM provides considerable user control over TR degeneracy and output filtration.

ISSN: 1471-2105