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Table 1 Comparison of programs for the detection of repetitive subsequences in proteins

From: Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

Program Method used Detection of degenerate repeats Calculation of a P-Value Analysis of whole Proteomes %Hits found in SwissProt Detection of T. brucei procyclin 1
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
  1. 1The T. brucei surface protein (GenBank accession AAK62893) with five GPEET repeats [25] was used for benchmarking.
  2. 2Word count using a hash table.
  3. 3Using P < 0.001 (same as for Internal Repeats Finder).