How to find simple and accurate rules for viral protease cleavage specificities

BMC Bioinformatics

Table 9 Applying the HCV NS3 rules to the NS3 in vivo test data.

Decamer	Rule match	Decamer	Rule match
DCYVYCSGSW	HCVA, HCVB, HCVC	DCSQPCAGSW	HCVA
DCAVTCSGSW	HCVA, HCVB	DCIIVCAGSW	HCVA, HCVB, HCVC
DCAVRCSGSW	HCVA, HCVB, HCVC	DCQQLCAGSW	HCVA
DCIKCCSGSW	-	DCPSPCAGSW	HCVA
DCVSNCSGSW	HCVA	DCAILCAGSW	HCVA, HCVB
DCVMKCSGSW	HCVA	DCIMPCAGSW	HCVA
DCATTCSGSW	HCVA, HCVB	DCVRMCAGSW	HCVA, HCVC
DCTQMCSGSW	HCVA	DCSVLCAGSW	HCVA
DCLDLCSGSW	HCVA	DCYRPCAGSW	HCVA, HCVB, HCVC
DCVTPCSGSW	HCVA, HCVC	DCLCLCAGSW	HCVA
DCVSLCSGSW	HCVA	DCAVCCAGSW	HCVA, HCVB
DCPLACSGSW	HCVA	DCPIMCAGSW	HCVA, HCVC
DCMCDCSGSW	HCVA	DCHQMCAGSW	HCVA
DCVLRCSGSW	HCVA	DCWTPCAGSW	HCVA, HCVB, HCVC
DCAVTCSGSW	HCVA, HCVB	DCIIKCCGSW	HCVA
DCSVRCSGSW	HCVA	DCIMECCGSW	HCVA
DCSHPCSGSW	HCVA	DCSQLCCGSW	HCVA
DCCVRCSGSW	HCVA, HCVB, HCVC	DCTVACTGSW	HCVA
DCSVLCSGSW	HCVA	DCLVACTGSW	HCVA
DCRVRCSGSW	HCVA, HCVB, HCVC	DCPCPCTGSW	HCVA
DCVTPCSGSW	HCVA, HCVC	DCLELCTGSW	HCVA
DCIYICSGSW	HCVA	DCLVACTGSW	HCVA
DCRLPCSGSW	HCVA, HCVB	DCQIICTGSW	HCVA
DCYERCSGSW	HCVA, HCVB, HCVC	DCVVCCGGSW	HCVA
DCAVLCSGSW	HCVA, HCVB	DCTVTTSGSW	HCVB
DCVRLCSGSW	HCVA	DCTVETSGSW	HCVB, HCVC
DCPTNCSGSW	HCVA, HCVC	DCSVVCSSSW	HCVA
DCPRLCSGSW	HCVA	DCSVACSQSW	HCVA
DCVSNCSGSW	HCVA	DCSTLCSTSW	HCVA
DCRIPCSGSW	HCVA, HCVB, HCVC	DCSITCAQSW	HCVA
DCVSNCSGSW	HCVA	DCSVLCARSW	HCVA
DCFAMCSGSW	HCVA	DCSVPCTGSW	HCVA
DCTIKCAGSW	HCVA, HCVB, HCVC	DCSLPCGSSW	HCVA
DCLITCAGSW	HCVA	DCSAPCGSSW	HCVA
DCKVTCAGSW	HCVA, HCVB	DCVVPCSGSW	HCVA, HCVC (*)

The table shows the result of applying the HCV NS3 cleavage rules to the 69 decamers listed as especially good substrates in vivo by Kim et al. [36]. The first and third column show the decamers and the second and fourth column show the HCV rules that it matches (if any). The last (70^th) sequence (DCVVPCSGSW), marked with (*), is the consensus sequence tested by Kim et al., this sequence is already in the HCV NS3 data set and is thus not an out-of-sample prediction.

ISSN: 1471-2105