Softberry releases annotation
of SARS associated coronavirus TOR2 with FGENESV viral gene finder and
FGENESV-Annotator script. To access annotation:
FGENESV algorithm is based on pattern recognition of different types of signals
and Markov chain models of coding regions. Optimal combination of these features
is then found by dynamic programming and a set of gene models is constructed
along given sequence.
FGENESV is the fastest ab initio viral gene prediction program available.
We developed new FGENESV-Annotator script that finds similar proteins in public
databases and annotates predicted genes. This script can also identify low
scoring genes if they have known homologous protein.
There are two variants of viral gene prediction program: FGENESV0, which is
suited for small (<10 kb) genomes, uses generic parameters of coding regions,
while FGENESV learns genome-specific parameters using viral genome sequence as
FGENESV predicts all intronless viral genes. To find small group of genes that
contain introns - normally alternative structures of intronless variants -
standard eukaryotic gene finding programs, such as FGENESH, can be used in
addition to FGENESV.
As additional parameters, you can choose Linear or Circular form of your virus
and select alternative genetic code (Standard code is default): The Bacterial
and Plant Plastid Code (transl_table=11) or The Mold, Protozoan, and
Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
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