ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

BMC Bioinformatics

Table 2 The numbers of annotated and additional genes found by ZCURVE_V and the GeneMark VIOLIN database, respectively, for the five genomes with particular features ^a

GenBank information			ZCURVE_V		GeneMark^b
Organisms	Chromosome sequence length (bp)	No. of annotated genes	No. of annotated genes found	No. of additional genes predicted	No. of annotated genes found	No. of additional genes predicted
CYDV-RPV satRNA	322	0	0	0	0	0
SatPaMV^c	826	2	2	0	1	0
SV-MWLMV	1168	1	1	0	0	1
SLRSV	1118	1	1	0	1	0
AmEPV	232,392	294	245	5	239	323

^a Of the five viral genomes, cereal yellow dwarf virus-RPV satellite RNA (CYDV-RPV satRNA), panicum mosaic satellite virus (satPaMV), satellite maize white line mosaic virus (SV-MWLMV) and strawberry latent ringspot virus satellite RNA (SLRSV) are less than or slightly larger than 1000 bp in length, whereas amsacta moorei entomopoxvirus (AmEPV) has probably the lowest GC content among the sequenced organisms (17.78%).
^b Data deposited in the GeneMark VIOLIN database are used.
^c For this genome, we adjusted the default settings, i.e., using the 'single-stranded virus' option.

ISSN: 1471-2105