The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats-0

<p><b>Copyright information:</b></p><p>Taken from "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats"</p><p>http://www.biomedcentral.com/1471-2105/8/172</p><p>BMC Bioinformatics 2007;8():172-172.</p><p>Published online 23 May 2007</p><p>PMCID:PMC1892036.</p><p></p>R observed only in NC_007503_3 is in red. CRISPR units (DR + spacer) are numbered on the left and spacers' length is indicated on the right

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats-1

<p><b>Copyright information:</b></p><p>Taken from "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats"</p><p>http://www.biomedcentral.com/1471-2105/8/172</p><p>BMC Bioinformatics 2007;8():172-172.</p><p>Published online 23 May 2007</p><p>PMCID:PMC1892036.</p><p></p

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats-2

<p><b>Copyright information:</b></p><p>Taken from "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats"</p><p>http://www.biomedcentral.com/1471-2105/8/172</p><p>BMC Bioinformatics 2007;8():172-172.</p><p>Published online 23 May 2007</p><p>PMCID:PMC1892036.</p><p></p>ey have only questionable CRISPRs and strains in yellow have no CRISPR. 2. General information on the CRISPR clusters and their location. 3. Detailed information on the clusters: DRs are in yellow, spacers are in random colours. 4. Link to the spacers fasta file

Genomic organization of phiC725A.

<p>A) Distribution of the predicted CDSs along the phage genome. CDSs are shown as horizontal arrows. Position 1 in the sequence is defined in keeping with phage F116. The different colors correspond to the putative function: red, DNA replication, modification and repair; orange, terminase; green, morphogenesis and packaging; light green, putative RNA polymerase; pink, lysis; blue, lysogeny control; yellow, unidentified. The vertical arrow indicates the putative localization of the <i>pac</i> site. The <i>att</i> site towards the right end is in the TCTCTCCGTCCGCACCA orientation, i.e. the reverse orientation with respect to the PAO1Or host sequence orientation. B) Mapping of the sequencing reads showing an excess at the level of the terminase subunits genes, with a progressive decrease towards the right end.</p

Distribution of packaged bacterial reads from C7-25 mitomycin C-induced phages.

<p>A) Mapping of the bacterial reads along the PAO1_Or genome. The blue horizontal arrow represents the prophage. B) Organization of the phiC725A prophage and close-up of the 800kb left flanking region; the distribution of the packaged bacterial sequence reads is shown. The collection of arrows underneath the graph and starting from the right at the tentative prophage <i>pac</i> site within the blue bar representing the phage genome, correspond to coverage maximums. The first such maximum is located approximately 25 kb from the left of the blue bar. The spacing between the arrows is approximately 72kb, compared to the 65 kb of phage genome suggesting that the terminal redundancy represents 10% of the phage size. The blue, black and yellow lines represent the minimum, average and maximum read coverage observed respectively.</p

Electron microscopy observation of phage phiC725A.

<p>The black bar represents 200nm.</p

Growth curve of uninfected PA14 (dark grey curve) and of PA14 infected by Ab31 at an M.O.I. of 0.1 (light grey curve).

<p>Growth curve of uninfected PA14 (dark grey curve) and of PA14 infected by Ab31 at an M.O.I. of 0.1 (light grey curve).</p

List of the strains used and susceptibility to Ab31.

a<p>UN, unknown.</p>b<p>5 μL of Ab31 stock suspension (≈ 10⁸PFU/ml) were spotted on <i>P. aeruginosa</i> lawns. C+++, complete clearing; trace, a few individual plaques; 0, a turbid spot where the pipette tip touched the agar.</p

Annotation of the Ab31 genome.

<p>The Ab31 hypothetical terminal ends are at the 1 position. The morphogenesis module includes proteins similar to those encoded by phage AF (red), whereas the replication, recombination and lysis modules consist of genes similar to those of phage PAJU2 (blue). Genes encoding hypothetical proteins which have homologies with other phages are shown in purple color. Genes encoding hypothetical proteins of unknown function are shown in green color.</p

List of coding sequences (CDS) and their position in the 234 kbp deleted region.

<p>List of coding sequences (CDS) and their position in the 234 kbp deleted region.</p