An intragenic distribution bias of DNA uptake sequences in Pasteurellaceae and Neisseriae

Additional file 1:

Total counts and fractions of the US in the genes of 7 Pasteurellaceae genomes. Total counts and percentages of the different motifs (the US 5'-AAAGTGCGGT-3' and rcUS 5'-ACCGCACTTT-3') in the coding regions of 7 Pasteurellaceae genomes (the accession numbers are given for each strain).

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Additional file 2:

The intragenic distribution of the Actinobacillus pleuropneumoniae uptake sequence.

The intragenic distribution of the alternative US (left three sub-graphs, increasing the motif stringency from 8 to 10 bases) and its reverse complement (next three sub-graphs, increasing the motif stringency from 8 to 10 bases) in the protein coding regions of Actinobacillus pleuropneumoniae (accession number NC_009053). The counts of the motifs are depicted underneath.

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Additional file 3:

The intragenic distribution of the Neisseria meningitidis uptake sequence. The intragenic distribution of the US and its reverse complement (rcUS) in the protein coding regions of Neisseria meningitidis MC58 (accession number NC_003112). Genes that start with the US are excluded. The sequence and the counts of the motifs are depicted underneath.

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Additional file 4:

US abundance in the coding fraction and total DNA of 5 representative Pasteurellaceae genomes. Counts of USs and rcUSs in the genomes of five Pasteurellaceae species (with their accession number and coding density according to NCBI), the counts in the coding sequences (CDS), the total genomic count (Total count), the percentage of motifs found in the CDS (% of total) and the counts of motifs found by Redfield et al. (2006).

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