Table 1

Comparison of programs for the detection of repetitive subsequences in proteins
Program
 Method used
 Detection of degenerate repeats
 Calculation of a P-Value
 Analysis of whole Proteomes
 %Hits found in SwissProt
 Detection of T. brucei procyclin1
Reptile
 Hashing2
 No
 Yes
 Yes
 153
 Yes
REP [2]
 Profiles of known repeats
 Yes
 No
 No
 1.1
 No
RADAR [5]
 Alignment
 Yes
 No
 No
 28
 Yes
REPRO [7]
 Alignment
 Yes
 No
 No
 n.a.
 Yes
Internal Repeats finder [8]
 Alignment
 Yes
 Yes
 No
 14
 No
TRIPS [9]
 Fourier transform
 Yes
 No
 No
 12
 No
RepSeq [10]
 Hashing
 Yes
 Yes
 Yes
 n.a.
 Yes
ProtRepeatsDB [11]
 Mixed
 Yes
 Yes
 Yes
 n.a.
 Yes
Repper [12]
 Fourier transform
 Yes
 No
 No
 n.a.
 No

1The T. brucei surface protein (GenBank accession AAK62893) with five GPEET repeats [25] was used for benchmarking.

2Word count using a hash table.

3Using P < 0.001 (same as for Internal Repeats Finder).

Fankhauser et al. Proteome Science 2007 5:20   doi:10.1186/1477-5956-5-20