Definition of Table Header

Organism IGS# Up stream Locus Up stream Product Down Stream Locus Down Stream Product Gene Dir type Start End IGS Len GC% IS NT IS AA NR PT-Pair Intra Spp. IGS Inter Spp. IGS Conserved Inter-spp IGS Start Conserved Inter-spp IGS End

Organism: organism abbreviation

  1. Actinobacillus actinomycetemcomitans: A. act
  2. Fusobacterium nucleatum: F. nuc
  3. Porphyromonas gingivalis: P. gin
  4. Prevotella intermedia: P. int
  5. Streptococcus mutans: S. mut
  6. Streptococcus mitis: S. mit
  7. Streptococcus sanguinis: S. san
  8. Tannerella forsythensis: T. for
  9. Treponema denticola: T. den

IGS#: Intergenic sequence (IGS) number

Upstream Locus: Locus tag of upstream gene

Upstream Product: Product of upstream gene

Downstream Locus: Locus tag of downstream gene

Downstream Product: Product of downstream gene

Gene Dir type: Directional type of upstream and downstream genes: H: Head, 5' end of CDS; T: Tail 3' end of CDS; HH (Head to Head ), HT (Head to Tail), TH (Tail to Head), TT (Tail to Tail)

Start/End: Start position and end position of IGS

IGS Len: Sequence length of IGS

GC%: GC percentage of corresponding IGS

IS-nt: Total hit of IGS against insertion element nucleotide database

IS-aa: Total hit of IGS against insertion element protein database

NR: Total hit of IGS against NR (non-redundant protein) database, left number: hit # of intra-species/ right number: hit # of other organism

IGS: Total hit of IGS against IGS Blast DB, left number: intra-species / right number: other organism

PT-Pair: Promoter and Rho-independent terminator information. Example: [+: 1/2/1 | -: 0/4/0] means, in positive strand, there are 1 promoter and 2 terminator, and they can form a promoter-terminator pair that longer than 50bps. In negative strand, there are 4 terminator but no promoter in this region, and there is no promoter-terminator pair in negative strand.

Intra Spp. IGS: Total intra-species hit of IGS against IGS database, this means the query IGS is conserved in self-genome.

Inter Spp. IGS: Total inter-species hit of IGS against IGS database, this means the query IGS is conserved in other organism and exclude itself.

Conserved Inter-spp IGS Start/End: Start and end position of conserved IGS from inter-species blast result.