Decodon - Exploring Life Exploring Life.

Which formats are accepted for Genome Views?

With version 2.1.3 Paver supports Genbank GFF format for creating Genome Views:

  • parent features (3rd column): 'gene' and the motifs
    • Promoter ( 'p' )
    • Terminator ( 't' )
    • RT Terminator ( 'rt' )
    • Regulator Binding Site ( 'regbs' )
    • Ribosome Binding Site ( 'rbs' )
    • Sequence Motif ( 'sm' )
  • keywords interpreted: (9th column): 'locus_tag=' and 'gene='

Genbank GFF:

super    NC_002951.2    gene    5605    6966    .    +    .    locus_tag=SACOL0001;product=chromosomal replication initiation protein;gene=dnaA
super    NC_002951.2    gene    7253    8386    .    +    .    locus_tag=SACOL0002;product=DNA polymerase III subunit beta;gene=dnaN
super    NC_002951.2    gene    15608    16309    .    -    .    locus_tag=SACOL0007;product=hypothetical protein;gene=nnrD
super    NC_002951.2    gene    21360    21689    .    +    .    locus_tag=SACOL0011;product=hypothetical protein
....

and a generic format:

bsub chromosome    rnpA    gene    4213777    4214127    -    BSU41050
bsub chromosome    rpmH    gene    4214279    4214413    -    BSU41060
bsub chromosome    Abh binding site    P    2269077    2269111    -    BSU21480
bsub chromosome    Abh binding site    P    3834967    3835065    +    BSU37350
bsub chromosome    dnaN    T    3086    3126    +    BSU00020
bsub chromosome    gyrB    T    6791    6837    +    BSU00060
....

Please copy the contents of an example area into an editor and replace every occurence of 4 consequent white spaces (' ') by a tabulator (tab, \t) to have technically working example snippet.

Go back

Add a comment

Subscribe to our newsletter: