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Open Access Research article

Homopolymeric tracts represent a general regulatory mechanism in prokaryotes

Renato H Orsi*, Barbara M Bowen and Martin Wiedmann

Author Affiliations

Department of Food Science, Cornell University, Ithaca, NY 14853, USA

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BMC Genomics 2010, 11:102  doi:10.1186/1471-2164-11-102

Published: 9 February 2010

Additional files

Additional file 1:

Distribution of homopolymeric tracts in coding genes of 99 prokaryotic chromosomes. Columns contain species name, NCBI accession numbers of their respective chromosomes, nucleotide frequencies, GC content, total length of the coding genes summed in each chromosome, total number of coding genes in each chromosome, observed and expected numbers and an associated Z-score for each HT in each chromosome.

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Additional file 2:

Distribution of homopolymeric tracts in Listeria monocytogenes strain EGD-e and Buchnera aphidicola strain Cc coding genes classified by role categories. Columns contain role categories for L. monocytogenes and B. aphidicola, nucleotide frequencies, GC content, total length of the coding genes summed in each role category, total number of coding genes in role category, observed and expected numbers and an associated Z-score for each HT in each role category.

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Additional file 3:

Frequency of indels in the L. monocytogenes inlA 5'polyA HT (as determined by translational kanamycin resistance reporter fusions). Summary of the translational kanamycin resistance reporter fusion results for three strains representing three different alleles of the 5'end HT found in L. monocytogenes inlA. Three replicates were carried out for each strain.

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Additional file 4:

Isolates used for sequence analysis of the inlA poly(A) HT. The table provides (i) isolate identification number, (ii) source, (iii) year of isolation, (iv) state and country of isolation, (v) lineage (I, II, III or IV), and (vi) EcoRI ribotype designations for the 105 L. monocytogenes isolates that were used to build a phylogeny of the 5'end of inlA (shown in Figure 4).

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Additional file 5:

Genomes sorted by G+C content. Genomes used for HT analyses sorted from the lowest to highest G+C content. This is the order used in Figure 1.

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