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

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 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

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).

ISSN: 1477-5956