MetaGeneAnnotator
2008/8/19
Hideki Noguchi
hide@cb.k.u-tokyo.ac.jp

MetaGene is a prokaryotic gene-finding program and can be widely applied to 
fragmented anonymous genomic sequences, such as metagenomic data.

MetaGeneAnnotator can predict phage genes in addition to bacterial and 
archaeal genes, and precisely predicts translation initiation sites of genes 
by using an RBS model.



usage: mga [multi-fasta] <-m/-s>
         -m: multiple species (sequences are individually treated)
         -s: single species (sequences are treated as a unit)

output format:
    # [sequence name]
    # gc = [gc%], rbs = [rbs%]
    # self: [(b)acteria/(a)rchaea/(p)hage/unused(-)]
    [gene ID] [start pos.] [end pos.] [strand] [frame] [complete/partial]
    [gene score] [used model] [rbs start] [rbs end] [rbs score]
    . . .
    . . .
    . . .

<explanations of output column>
    *The value of [frame] (0/1/2) indicates the number of surplus
    (untranslated) nucleotides at the 5'-end of the predicted ORF.
    *The value of [score] indicates the estimated score of predicted gene. All
    predicted genes are more than 0.
    *The value of [complete/partial] indicates that the predicted gene
    structure is whether complete (contains both of start and stop codons[11])
    or partial (lacks start[01] or stop[10] or both of them[00]).
    *The value of [model] indicates a selected model
    ((s)elf/(b)acteria/(a)rchaea/(p)hage) for predicting the gene. 
