RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses

Table 2 Strains detected from amino acid sequences of noro and enterovirus capsids

Input amino acid				Output
Complete capsid sequence		Partial capsid sequence		Detected strains corresponding to input cols
Col (1) Noro	Col (2) Entero	Col (3) Noro	Col (4) Entero	Col (1) Noro	Col (2) Entero	Col (3) Noro	Col (4) Entero
Seacroft [AJ277620]	Polio_2 [DQ841140]	1UK1 [DQ665819]	Cox-B5 [AF114383]	Minireovirus [U02030]	Polio_3 [AF448782]	Beeskow [Q915C5]	Cox-B5 [AF114383]
Appalachicola [AF414406]	Simian_A [NP_714932]	2JP1 [AB264170]	Echo-11 [AB239122]	Chiba [AB042808]	Simian-7 [AF326759]	Chiba [AB042808]	Echo-11 [AF081326]
Baltimore_a [AF414408]	HEV-D [NP_740741]	3JP2 [AB264158]	Echo-13 [AB239091]	Minireovirus [U02030]	HEV-D [D17595]	Norwalk [1IHM]	Echo-13 [AF081327]
Baltimore_b [AF414404]	HEV-71 [AAY59418]	4JP3 [AB264152]	HEV-B [DQ842180]	Chiba [AB042808]	HEV-A71 [AF135944]	Potsdam [AF439267]	Cox-B3 [AF231763]
Boxer [AF538679]	Cox-B5 [AAW71476]	5TP1 [DQ263739]	HEV-75 [DQ468142]	Potsdam [AF439267]	Cox_B5 [AF114383]	Bitburg [AF427112]	Proposed HEV-75 [AF152298]

Input complete capsid sequences are shown in cols 1 and 2 while the input partial sequences are shown in cols 3 and 4. The corresponding closest database strains detected by the program are shown in the last 4 cols whose headers are color matched with those of the input sequence cols. The NCBI accession codes are enclosed within square brackets for all capsid sequences except for Norwalk virus whose PDB code is correspondingly shown. The enterovirus capsid sequences refer to those of VP1 subunits. Abbreviations used: HEV: Human enterovirus; Cox; Coxsackievirus.

ISSN: 1471-2105